# Copyright 2008 by Peter Cock. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Align.stockholm module.""" import unittest from io import StringIO from Bio import Align try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.stockholm." ) from None class TestStockholm_reading(unittest.TestCase): def test_reading_example(self): """Test parsing Pfam record HAT as the docstring example.""" path = "Stockholm/example.sth" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertEqual(alignment.annotations["identifier"], "HAT") self.assertEqual(alignment.annotations["accession"], "PF02184.18") self.assertEqual(alignment.annotations["definition"], "HAT (Half-A-TPR) repeat") self.assertEqual(alignment.annotations["author"], ["SMART;"]) self.assertEqual( alignment.annotations["source of seed"], "Alignment kindly provided by SMART", ) self.assertEqual(alignment.annotations["gathering method"], "21.00 21.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "21.00 21.00;") self.assertEqual(alignment.annotations["noise cutoff"], "20.90 20.90;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Repeat") self.assertEqual(alignment.annotations["clan"], "CL0020") self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "9478129") self.assertEqual( alignment.annotations["references"][0]["title"], "The HAT helix, a repetitive motif implicated in RNA processing.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Preker PJ, Keller W;" ) self.assertEqual( alignment.annotations["references"][0]["location"], "Trends Biochem Sci 1998;23:15-16.", ) self.assertEqual(len(alignment.annotations["database references"]), 3) self.assertEqual( alignment.annotations["database references"][0], {"reference": "INTERPRO; IPR003107;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "SMART; HAT;"}, ) self.assertEqual( alignment.annotations["database references"][2], {"reference": "SO; 0001068; polypeptide_repeat;"}, ) self.assertEqual( alignment.annotations["comment"], "The HAT (Half A TPR) repeat is found in several RNA processing proteins [1].", ) self.assertEqual(len(alignment.sequences), 3) self.assertEqual(alignment.sequences[0].annotations["accession"], "P17886.2") self.assertEqual(alignment.sequences[1].annotations["accession"], "P87312.1") self.assertEqual(alignment.sequences[1].dbxrefs, ["PDB; 3JB9 R; 185-216;"]) self.assertEqual(alignment.sequences[2].annotations["accession"], "O16376.2") self.assertEqual(alignment.sequences[0].id, "CRN_DROME/191-222") self.assertEqual(alignment.sequences[1].id, "CLF1_SCHPO/185-216") self.assertEqual(alignment.sequences[2].id, "O16376_CAEEL/201-233") self.assertEqual(alignment[0], "KEIDRAREIYERFVYVH-PDVKNWIKFARFEES") self.assertEqual(alignment[1], "HENERARGIYERFVVVH-PEVTNWLRWARFEEE") self.assertEqual(alignment[2], "KEIDRARSVYQRFLHVHGINVQNWIKYAKFEER") self.assertEqual(alignment.sequences[0].seq, "KEIDRAREIYERFVYVHPDVKNWIKFARFEES") self.assertEqual(alignment.sequences[1].seq, "HENERARGIYERFVVVHPEVTNWLRWARFEEE") self.assertEqual( alignment.sequences[1].letter_annotations["secondary structure"], "--HHHHHHHHHHHHHHS--HHHHHHHHHHHHH", ) self.assertEqual( alignment.sequences[2].seq, "KEIDRARSVYQRFLHVHGINVQNWIKYAKFEER" ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], "--HHHHHHHHHHHHHHS.--HHHHHHHHHHHHH", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "KEIDRARuIYERFVaVH.P-VpNWIKaARFEEc", ) def check_alignment_globins45(self, alignment): """Check the alignment obtained by parsing hmmalign output.""" self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[0, 0, 0, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 51, 55, 78, 78, 79, 80, 146, 147, 148, 153], [0, 1, 1, 1, 1, 13, 15, 42, 43, 46, 46, 50, 73, 73, 74, 75, 141, 142, 143, 148], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 0, 0, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 1, 1, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 1, 1, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 1, 1, 1, 5, 17, 19, 46, 46, 49, 49, 49, 72, 73, 74, 74, 140, 141, 141, 141], [0, 1, 1, 1, 5, 17, 19, 46, 47, 50, 50, 50, 73, 74, 75, 75, 141, 142, 142, 142], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 145, 146, 146], [0, 1, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 146, 146, 146], [0, 0, 1, 2, 6, 18, 18, 45, 46, 49, 50, 54, 77, 78, 79, 79, 145, 145, 145, 145], ] # fmt: on ), ) ) self.assertEqual(alignment.sequences[0].id, "MYG_ESCGI") self.assertEqual( alignment.sequences[0].seq, "VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKelgfqg", ) self.assertEqual( alignment.sequences[0].letter_annotations["posterior probability"], "69****************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[1].id, "MYG_HORSE") self.assertEqual( alignment.sequences[1].seq, "gLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKelgfqg", ) self.assertEqual( alignment.sequences[1].letter_annotations["posterior probability"], "889***************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[2].id, "MYG_PROGU") self.assertEqual( alignment.sequences[2].seq, "gLSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLKAEDEMRASEELKKHGTTVLTALGGILKKKGQHAAELAPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKelgfqg", ) self.assertEqual( alignment.sequences[2].letter_annotations["posterior probability"], "889***************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[3].id, "MYG_SAISC") self.assertEqual( alignment.sequences[3].seq, "gLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASEELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKelgfqg", ) self.assertEqual( alignment.sequences[3].letter_annotations["posterior probability"], "889***************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[4].id, "MYG_LYCPI") self.assertEqual( alignment.sequences[4].seq, "gLSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKelgfqg", ) self.assertEqual( alignment.sequences[4].letter_annotations["posterior probability"], "889***************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[5].id, "MYG_MOUSE") self.assertEqual( alignment.sequences[5].seq, "gLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSEDLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKelgfqg", ) self.assertEqual( alignment.sequences[5].letter_annotations["posterior probability"], "889***************************************************************************99******************************************************************7******", ) self.assertEqual(alignment.sequences[6].id, "MYG_MUSAN") self.assertEqual( alignment.sequences[6].seq, "vDWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKSLGELKDTADIKAQADTVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKaanfqg", ) self.assertEqual( alignment.sequences[6].letter_annotations["posterior probability"], "789***************************************987789*************************99****************************************************************997******", ) self.assertEqual(alignment.sequences[7].id, "HBA_AILME") self.assertEqual( alignment.sequences[7].seq, "VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSPGSAQVKAHGKKVADALTTAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR", ) self.assertEqual( alignment.sequences[7].letter_annotations["posterior probability"], "69********************************************9**9***********************9******************************************************************7", ) self.assertEqual(alignment.sequences[8].id, "HBA_PROLO") self.assertEqual( alignment.sequences[8].seq, "VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSPGSAQVKAHGKKVADALTLAVGHLDDLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR", ) self.assertEqual( alignment.sequences[8].letter_annotations["posterior probability"], "69********************************************9**9***********************9******************************************************************7", ) self.assertEqual(alignment.sequences[9].id, "HBA_PAGLA") self.assertEqual( alignment.sequences[9].seq, "VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHFDLSHGSAQVKAHGKKVADALTLAVGHLEDLPNALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR", ) self.assertEqual( alignment.sequences[9].letter_annotations["posterior probability"], "69**********************************************************************989*****************************************************************7", ) self.assertEqual(alignment.sequences[10].id, "HBA_MACFA") self.assertEqual( alignment.sequences[10].seq, "VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR", ) self.assertEqual( alignment.sequences[10].letter_annotations["posterior probability"], "69***********************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[11].id, "HBA_MACSI") self.assertEqual( alignment.sequences[11].seq, "VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR", ) self.assertEqual( alignment.sequences[11].letter_annotations["posterior probability"], "69***********************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[12].id, "HBA_PONPY") self.assertEqual( alignment.sequences[12].seq, "VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKDHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR", ) self.assertEqual( alignment.sequences[12].letter_annotations["posterior probability"], "69***********************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[13].id, "HBA2_GALCR") self.assertEqual( alignment.sequences[13].seq, "VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSHGSTQVKGHGKKVADALTNAVLHVDDMPSALSALSDLHAHKLRVDPVNFKLLRHCLLVTLACHHPAEFTPAVHASLDKFMASVSTVLTSKYR", ) self.assertEqual( alignment.sequences[13].letter_annotations["posterior probability"], "69***********************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[14].id, "HBA_MESAU") self.assertEqual( alignment.sequences[14].seq, "VLSAKDKTNISEAWGKIGGHAGEYGAEALERMFFVYPTTKTYFPHFDVSHGSAQVKGHGKKVADALTNAVGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPADFTPAVHASLDKFFASVSTVLTSKYR", ) self.assertEqual( alignment.sequences[14].letter_annotations["posterior probability"], "69********************************************888************************9******************************************************************7", ) self.assertEqual(alignment.sequences[15].id, "HBA2_BOSMU") self.assertEqual( alignment.sequences[15].seq, "VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR", ) self.assertEqual( alignment.sequences[15].letter_annotations["posterior probability"], "69***********************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[16].id, "HBA_ERIEU") self.assertEqual( alignment.sequences[16].seq, "VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHFDLNPGSAQVKGHGKKVADALTTAVNNLDDVPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLALHHPADFTPAVHASLDKFLATVATVLTSKYR", ) self.assertEqual( alignment.sequences[16].letter_annotations["posterior probability"], "69********************************************9999***********************99*****************************************************************7", ) self.assertEqual(alignment.sequences[17].id, "HBA_FRAPO") self.assertEqual( alignment.sequences[17].seq, "VLSAADKNNVKGIFGKISSHAEDYGAEALERMFITYPSTKTYFPHFDLSHGSAQVKGHGKKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGNVLTAKYR", ) self.assertEqual( alignment.sequences[17].letter_annotations["posterior probability"], "69***********************************************************************99*****************************************************************7", ) self.assertEqual(alignment.sequences[18].id, "HBA_PHACO") self.assertEqual( alignment.sequences[18].seq, "VLSAADKNNVKGIFTKIAGHAEEYGAEALERMFITYPSTKTYFPHFDLSHGSAQIKGHGKKVVAALIEAVNHIDDITGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGTVLTAKYR", ) self.assertEqual( alignment.sequences[18].letter_annotations["posterior probability"], "69***********************************************************************99*****************************************************************7", ) self.assertEqual(alignment.sequences[19].id, "HBA_TRIOC") self.assertEqual( alignment.sequences[19].seq, "VLSANDKTNVKTVFTKITGHAEDYGAETLERMFITYPPTKTYFPHFDLHHGSAQIKAHGKKVVGALIEAVNHIDDIAGALSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPSVLTPEVHASLDKFLCAVGNVLSAKYR", ) self.assertEqual( alignment.sequences[19].letter_annotations["posterior probability"], "69********************************************999************************99*****************************************************************7", ) self.assertEqual(alignment.sequences[20].id, "HBA_ANSSE") self.assertEqual( alignment.sequences[20].seq, "VLSAADKGNVKTVFGKIGGHAEEYGAETLQRMFQTFPQTKTYFPHFDLQPGSAQIKAHGKKVAAALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKFLGHCFLVVLAIHHPSLLTPEVHASMDKFLCAVATVLTAKYR", ) self.assertEqual( alignment.sequences[20].letter_annotations["posterior probability"], "69********************************************9999***********************99*****************************************************************7", ) self.assertEqual(alignment.sequences[21].id, "HBA_COLLI") self.assertEqual( alignment.sequences[21].seq, "VLSANDKSNVKAVFAKIGGQAGDLGGEALERLFITYPQTKTYFPHFDLSHGSAQIKGHGKKVAEALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKLLGHCFLVVVAVHFPSLLTPEVHASLDKFVLAVGTVLTAKYR", ) self.assertEqual( alignment.sequences[21].letter_annotations["posterior probability"], "69***********************************************************************99*****************************************************************7", ) self.assertEqual(alignment.sequences[22].id, "HBAD_CHLME") self.assertEqual( alignment.sequences[22].seq, "mLTADDKKLLTQLWEKVAGHQEEFGSEALQRMFLTYPQTKTYFPHFDLHPGSEQVRGHGKKVAAALGNAVKSLDNLSQALSELSNLHAYNLRVDPANFKLLAQCFQVVLATHLGKDYSPEMHAAFDKFLSAVAAVLAEKYR", ) self.assertEqual( alignment.sequences[22].letter_annotations["posterior probability"], "689*******************************************9999******************************************************************************************7", ) self.assertEqual(alignment.sequences[23].id, "HBAD_PASMO") self.assertEqual( alignment.sequences[23].seq, "mLTAEDKKLIQQIWGKLGGAEEEIGADALWRMFHSYPSTKTYFPHFDLSQGSDQIRGHGKKVVAALSNAIKNLDNLSQALSELSNLHAYNLRVDPVNFKFLSQCLQVSLATRLGKEYSPEVHSAVDKFMSAVASVLAEKYR", ) self.assertEqual( alignment.sequences[23].letter_annotations["posterior probability"], "699*******************************************9**9******************************************************************************************7", ) self.assertEqual(alignment.sequences[24].id, "HBAZ_HORSE") self.assertEqual( alignment.sequences[24].seq, "sLTKAERTMVVSIWGKISMQADAVGTEALQRLFSSYPQTKTYFPHFDLHEGSPQLRAHGSKVAAAVGDAVKSIDNVAGALAKLSELHAYILRVDPVNFKFLSHCLLVTLASRLPADFTADAHAAWDKFLSIVSSVLTEKYR", ) self.assertEqual( alignment.sequences[24].letter_annotations["posterior probability"], "689*******************************************9999******************************************************************************************7", ) self.assertEqual(alignment.sequences[25].id, "HBA4_SALIR") self.assertEqual( alignment.sequences[25].seq, "sLSAKDKANVKAIWGKILPKSDEIGEQALSRMLVVYPQTKAYFSHWASVAPGSAPVKKHGITIMNQIDDCVGHMDDLFGFLTKLSELHATKLRVDPTNFKILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR", ) self.assertEqual( alignment.sequences[25].letter_annotations["posterior probability"], "69********************************************77769************************9*****************************************************************7", ) self.assertEqual(alignment.sequences[26].id, "HBB_ORNAN") self.assertEqual( alignment.sequences[26].seq, "VHLSGGEKSAVTNLWGKVNINELGGEALGRLLVVYPWTQRFFEAFGDLSSAGAVMGNPKVKAHGAKVLTSFGDALKNLDDLKGTFAKLSELHCDKLHVDPENFNRLGNVLIVVLARHFSKDFSPEVQAAWQKLVSGVAHALGHKYH", ) self.assertEqual( alignment.sequences[26].letter_annotations["posterior probability"], "69****************************************************************************9******************************************************************7", ) self.assertEqual(alignment.sequences[27].id, "HBB_TACAC") self.assertEqual( alignment.sequences[27].seq, "VHLSGSEKTAVTNLWGHVNVNELGGEALGRLLVVYPWTQRFFESFGDLSSADAVMGNAKVKAHGAKVLTSFGDALKNLDNLKGTFAKLSELHCDKLHVDPENFNRLGNVLVVVLARHFSKEFTPEAQAAWQKLVSGVSHALAHKYH", ) self.assertEqual( alignment.sequences[27].letter_annotations["posterior probability"], "69***********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[28].id, "HBE_PONPY") self.assertEqual( alignment.sequences[28].seq, "VHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNMDNLKTTFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH", ) self.assertEqual( alignment.sequences[28].letter_annotations["posterior probability"], "5789*********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[29].id, "HBB_SPECI") self.assertEqual( alignment.sequences[29].seq, "VHLSDGEKNAISTAWGKVHAAEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[29].letter_annotations["posterior probability"], "69****************99*****************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[30].id, "HBB_SPETO") self.assertEqual( alignment.sequences[30].seq, "VHLTDGEKNAISTAWGKVNAAEIGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALSHKYH", ) self.assertEqual( alignment.sequences[30].letter_annotations["posterior probability"], "69****************99*****************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[31].id, "HBB_EQUHE") self.assertEqual( alignment.sequences[31].seq, "vQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPAAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAQLSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[31].letter_annotations["posterior probability"], "579***************99*****************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[32].id, "HBB_SUNMU") self.assertEqual( alignment.sequences[32].seq, "VHLSGEEKACVTGLWGKVNEDEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNPKVKAHGKKVLHSLGEGVANLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVVVLASKFGKEFTPPVQAAFQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[32].letter_annotations["posterior probability"], "69****************99*****************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[33].id, "HBB_CALAR") self.assertEqual( alignment.sequences[33].seq, "VHLTGEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMNNPKVKAHGKKVLGAFSDGLTHLDNLKGTFAHLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPVVQAAYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[33].letter_annotations["posterior probability"], "689**********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[34].id, "HBB_MANSP") self.assertEqual( alignment.sequences[34].seq, "VHLTPEEKTAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPDAVMGNPKVKAHGKKVLGAFSDGLNHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[34].letter_annotations["posterior probability"], "69***********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[35].id, "HBB_URSMA") self.assertEqual( alignment.sequences[35].seq, "VHLTGEEKSLVTGLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSADAIMNNPKVKAHGKKVLNSFSDGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[35].letter_annotations["posterior probability"], "689**********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[36].id, "HBB_RABIT") self.assertEqual( alignment.sequences[36].seq, "VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[36].letter_annotations["posterior probability"], "69***********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[37].id, "HBB_TUPGL") self.assertEqual( alignment.sequences[37].seq, "VHLSGEEKAAVTGLWGKVDLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[37].letter_annotations["posterior probability"], "69***********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[38].id, "HBB_TRIIN") self.assertEqual( alignment.sequences[38].seq, "VHLTPEEKALVIGLWAKVNVKEYGGEALGRLLVVYPWTQRFFEHFGDLSSASAIMNNPKVKAHGEKVFTSFGDGLKHLEDLKGAFAELSELHCDKLHVDPENFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH", ) self.assertEqual( alignment.sequences[38].letter_annotations["posterior probability"], "69***************************************************************************989*****************************************************************7", ) self.assertEqual(alignment.sequences[39].id, "HBB_COLLI") self.assertEqual( alignment.sequences[39].seq, "vHWSAEEKQLITSIWGKVNVADCGAEALARLLIVYPWTQRFFSSFGNLSSATAISGNPNVKAHGKKVLTSFGDAVKNLDNIKGTFAQLSELHCDKLHVDPENFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH", ) self.assertEqual( alignment.sequences[39].letter_annotations["posterior probability"], "5779*********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[40].id, "HBB_LARRI") self.assertEqual( alignment.sequences[40].seq, "vHWSAEEKQLITGLWGKVNVADCGAEALARLLIVYPWTQRFFASFGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLDNIKNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH", ) self.assertEqual( alignment.sequences[40].letter_annotations["posterior probability"], "5779*********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[41].id, "HBB1_VAREX") self.assertEqual( alignment.sequences[41].seq, "vHWTAEEKQLICSLWGKIDVGLIGGETLAGLLVIYPWTQRQFSHFGNLSSPTAIAGNPRVKAHGKKVLTSFGDAIKNLDNIKDTFAKLSELHCDKLHVDPTNFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH", ) self.assertEqual( alignment.sequences[41].letter_annotations["posterior probability"], "66799********************************************************************************************************************************************7", ) self.assertEqual(alignment.sequences[42].id, "HBB2_XENTR") self.assertEqual( alignment.sequences[42].seq, "vHWTAEEKATIASVWGKVDIEQDGHDALSRLLVVYPWTQRYFSSFGNLSNVSAVSGNVKVKAHGNKVLSAVGSAIQHLDDVKSHLKGLSKSHAEDLHVDPENFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGYf", ) self.assertEqual( alignment.sequences[42].letter_annotations["posterior probability"], "66799*************************************************************************99*************************************************************99889", ) self.assertEqual(alignment.sequences[43].id, "HBBL_RANCA") self.assertEqual( alignment.sequences[43].seq, "vHWTAEEKAVINSVWQKVDVEQDGHEALTRLFIVYPWTQRYFSTFGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLDDVKGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH", ) self.assertEqual( alignment.sequences[43].letter_annotations["posterior probability"], "66799*************************************************************************99*****************************************************************7", ) self.assertEqual(alignment.sequences[44].id, "HBB2_TRICR") self.assertEqual( alignment.sequences[44].seq, "VHLTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY", ) self.assertEqual( alignment.sequences[44].letter_annotations["posterior probability"], "69*******************************************************************************************************************************************9988", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], ".xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......", ) self.assertEqual( alignment.column_annotations["consensus posterior probability"], ".679*****************************************************************************99******************************************************************7......", ) self.assertEqual( str(alignment), """\ MYG_ESCGI 0 --VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKAS MYG_HORSE 0 g--LSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKAS MYG_PROGU 0 g--LSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLKAEDEMRAS MYG_SAISC 0 g--LSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKAS MYG_LYCPI 0 g--LSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGS MYG_MOUSE 0 g--LSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGS MYG_MUSAN 0 v------DWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDT HBA_AILME 0 --VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGS HBA_PROLO 0 --VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGS HBA_PAGLA 0 --VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHF-DLS-----HGS HBA_MACFA 0 --VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGS HBA_MACSI 0 --VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGS HBA_PONPY 0 --VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGS HBA2_GALC 0 --VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGS HBA_MESAU 0 --VLSAKDKTNISEAWGKIGGHAGEYGAEALERMFFVYPTTKTYFPHF-DVS-----HGS HBA2_BOSM 0 --VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGS HBA_ERIEU 0 --VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHF-DLN-----PGS HBA_FRAPO 0 --VLSAADKNNVKGIFGKISSHAEDYGAEALERMFITYPSTKTYFPHF-DLS-----HGS HBA_PHACO 0 --VLSAADKNNVKGIFTKIAGHAEEYGAEALERMFITYPSTKTYFPHF-DLS-----HGS HBA_TRIOC 0 --VLSANDKTNVKTVFTKITGHAEDYGAETLERMFITYPPTKTYFPHF-DLH-----HGS HBA_ANSSE 0 --VLSAADKGNVKTVFGKIGGHAEEYGAETLQRMFQTFPQTKTYFPHF-DLQ-----PGS HBA_COLLI 0 --VLSANDKSNVKAVFAKIGGQAGDLGGEALERLFITYPQTKTYFPHF-DLS-----HGS HBAD_CHLM 0 m--LTADDKKLLTQLWEKVAGHQEEFGSEALQRMFLTYPQTKTYFPHF-DLH-----PGS HBAD_PASM 0 m--LTAEDKKLIQQIWGKLGGAEEEIGADALWRMFHSYPSTKTYFPHF-DLS-----QGS HBAZ_HORS 0 s--LTKAERTMVVSIWGKISMQADAVGTEALQRLFSSYPQTKTYFPHF-DLH-----EGS HBA4_SALI 0 s--LSAKDKANVKAIWGKILPKSDEIGEQALSRMLVVYPQTKAYFSHWASVA-----PGS HBB_ORNAN 0 -VHLSGGEKSAVTNLWGKV--NINELGGEALGRLLVVYPWTQRFFEAFGDLSSAGAVMGN HBB_TACAC 0 -VHLSGSEKTAVTNLWGHV--NVNELGGEALGRLLVVYPWTQRFFESFGDLSSADAVMGN HBE_PONPY 0 -VHFTAEEKAAVTSLWSKM--NVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGN HBB_SPECI 0 -VHLSDGEKNAISTAWGKV--HAAEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGN HBB_SPETO 0 -VHLTDGEKNAISTAWGKV--NAAEIGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGN HBB_EQUHE 0 v-QLSGEEKAAVLALWDKV--NEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPAAVMGN HBB_SUNMU 0 -VHLSGEEKACVTGLWGKV--NEDEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGN HBB_CALAR 0 -VHLTGEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMNN HBB_MANSP 0 -VHLTPEEKTAVTTLWGKV--NVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPDAVMGN HBB_URSMA 0 -VHLTGEEKSLVTGLWGKV--NVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSADAIMNN HBB_RABIT 0 -VHLSSEEKSAVTALWGKV--NVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNN HBB_TUPGL 0 -VHLSGEEKAAVTGLWGKV--DLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSSPSAVMSN HBB_TRIIN 0 -VHLTPEEKALVIGLWAKV--NVKEYGGEALGRLLVVYPWTQRFFEHFGDLSSASAIMNN HBB_COLLI 0 v-HWSAEEKQLITSIWGKV--NVADCGAEALARLLIVYPWTQRFFSSFGNLSSATAISGN HBB_LARRI 0 v-HWSAEEKQLITGLWGKV--NVADCGAEALARLLIVYPWTQRFFASFGNLSSPTAINGN HBB1_VARE 0 v-HWTAEEKQLICSLWGKI--DVGLIGGETLAGLLVIYPWTQRQFSHFGNLSSPTAIAGN HBB2_XENT 0 v-HWTAEEKATIASVWGKV--DIEQDGHDALSRLLVVYPWTQRYFSSFGNLSNVSAVSGN HBBL_RANC 0 v-HWTAEEKAVINSVWQKV--DVEQDGHEALTRLFIVYPWTQRYFSTFGDLSSPAAIAGN HBB2_TRIC 0 -VHLTAEDRKEIAAILGKV--NVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRN MYG_ESCGI 58 EDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHS MYG_HORSE 58 EDLKKHGTVVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHS MYG_PROGU 58 EELKKHGTTVLTALGGILKK-KGQHAAELAPLAQSHATKHKIPVKYLEFISEAIIQVLQS MYG_SAISC 58 EELKKHGTTVLTALGGILKK-KGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQK MYG_LYCPI 58 EDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQN MYG_MOUSE 58 EDLKKHGCTVLTALGTILKK-KGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKK MYG_MUSAN 53 ADIKAQADTVLSALGNIVKK-KGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSE HBA_AILME 52 AQVKAHGKKVADALTTAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAS HBA_PROLO 52 AQVKAHGKKVADALTLAVGHLD-DLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLAC HBA_PAGLA 52 AQVKAHGKKVADALTLAVGHLE-DLPNALSALSDLHAYKLRVDPVNFKLLSHCLLVTLAC HBA_MACFA 52 AQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAA HBA_MACSI 52 AQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAA HBA_PONPY 52 AQVKDHGKKVADALTNAVAHVD-DMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAA HBA2_GALC 52 TQVKGHGKKVADALTNAVLHVD-DMPSALSALSDLHAHKLRVDPVNFKLLRHCLLVTLAC HBA_MESAU 52 AQVKGHGKKVADALTNAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAN HBA2_BOSM 52 AQVKGHGAKVAAALTKAVGHLD-DLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLAS HBA_ERIEU 52 AQVKGHGKKVADALTTAVNNLD-DVPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAL HBA_FRAPO 52 AQVKGHGKKVVAALIEAANHID-DIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAI HBA_PHACO 52 AQIKGHGKKVVAALIEAVNHID-DITGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAI HBA_TRIOC 52 AQIKAHGKKVVGALIEAVNHID-DIAGALSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAI HBA_ANSSE 52 AQIKAHGKKVAAALVEAANHID-DIAGALSKLSDLHAQKLRVDPVNFKFLGHCFLVVLAI HBA_COLLI 52 AQIKGHGKKVAEALVEAANHID-DIAGALSKLSDLHAQKLRVDPVNFKLLGHCFLVVVAV HBAD_CHLM 52 EQVRGHGKKVAAALGNAVKSLD-NLSQALSELSNLHAYNLRVDPANFKLLAQCFQVVLAT HBAD_PASM 52 DQIRGHGKKVVAALSNAIKNLD-NLSQALSELSNLHAYNLRVDPVNFKFLSQCLQVSLAT HBAZ_HORS 52 PQLRAHGSKVAAAVGDAVKSID-NVAGALAKLSELHAYILRVDPVNFKFLSHCLLVTLAS HBA4_SALI 53 APVKKHGITIMNQIDDCVGHMD-DLFGFLTKLSELHATKLRVDPTNFKILAHNLIVVIAA HBB_ORNAN 57 PKVKAHGAKVLTSFGDALKNLD-DLKGTFAKLSELHCDKLHVDPENFNRLGNVLIVVLAR HBB_TACAC 57 AKVKAHGAKVLTSFGDALKNLD-NLKGTFAKLSELHCDKLHVDPENFNRLGNVLVVVLAR HBE_PONPY 57 PKVKAHGKKVLTSFGDAIKNMD-NLKTTFAKLSELHCDKLHVDPENFKLLGNVMVIILAT HBB_SPECI 57 AKVKAHGKKVIDSFSNGLKHLD-NLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAH HBB_SPETO 57 AKVKAHGKKVIDSFSNGLKHLD-NLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAH HBB_EQUHE 57 PKVKAHGKKVLHSFGEGVHHLD-NLKGTFAQLSELHCDKLHVDPENFRLLGNVLVVVLAR HBB_SUNMU 57 PKVKAHGKKVLHSLGEGVANLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVVVLAS HBB_CALAR 57 PKVKAHGKKVLGAFSDGLTHLD-NLKGTFAHLSELHCDKLHVDPENFRLLGNVLVCVLAH HBB_MANSP 57 PKVKAHGKKVLGAFSDGLNHLD-NLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAH HBB_URSMA 57 PKVKAHGKKVLNSFSDGLKNLD-NLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAH HBB_RABIT 57 PKVKAHGKKVLAAFSEGLSHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSH HBB_TUPGL 57 PKVKAHGKKVLTSFSDGLNHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLAC HBB_TRIIN 57 PKVKAHGEKVFTSFGDGLKHLE-DLKGAFAELSELHCDKLHVDPENFRLLGNVLVCVLAR HBB_COLLI 57 PNVKAHGKKVLTSFGDAVKNLD-NIKGTFAQLSELHCDKLHVDPENFRLLGDILVIILAA HBB_LARRI 57 PMVRAHGKKVLTSFGEAVKNLD-NIKNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAA HBB1_VARE 57 PRVKAHGKKVLTSFGDAIKNLD-NIKDTFAKLSELHCDKLHVDPTNFKLLGNVLVIVLAD HBB2_XENT 57 VKVKAHGNKVLSAVGSAIQHLD-DVKSHLKGLSKSHAEDLHVDPENFKRLADVLVIVLAA HBBL_RANC 57 PKVHAHGKKILGAIDNAIHNLD-DVKGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGA HBB2_TRIC 57 PKVLAHGAKVMRSIVEATKHLD-NLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLAL MYG_ESCGI 117 RHPGDFGADAQAAMNKALELFRKDIAAKYKelgfqg 153 MYG_HORSE 117 KHPGNFGADAQGAMTKALELFRNDIAAKYKelgfqg 153 MYG_PROGU 117 KHPGDFGADAQGAMSKALELFRNDIAAKYKelgfqg 153 MYG_SAISC 117 KHPGDFGADAQGAMKKALELFRNDMAAKYKelgfqg 153 MYG_LYCPI 117 KHSGDFHADTEAAMKKALELFRNDIAAKYKelgfqg 153 MYG_MOUSE 117 RHSGDFGADAQGAMSKALELFRNDIAAKYKelgfqg 153 MYG_MUSAN 112 MYPSEMNAQVQAAFSGAFKIICSDIEKEYKaanfqg 148 HBA_AILME 111 HHPAEFTPAVHASLDKFFSAVSTVLTSKYR------ 141 HBA_PROLO 111 HHPAEFTPAVHASLDKFFTSVSTVLTSKYR------ 141 HBA_PAGLA 111 HHPAEFTPAVHSALDKFFSAVSTVLTSKYR------ 141 HBA_MACFA 111 HLPAEFTPAVHASLDKFLASVSTVLTSKYR------ 141 HBA_MACSI 111 HLPAEFTPAVHASLDKFLASVSTVLTSKYR------ 141 HBA_PONPY 111 HLPAEFTPAVHASLDKFLASVSTVLTSKYR------ 141 HBA2_GALC 111 HHPAEFTPAVHASLDKFMASVSTVLTSKYR------ 141 HBA_MESAU 111 HHPADFTPAVHASLDKFFASVSTVLTSKYR------ 141 HBA2_BOSM 111 HLPSDFTPAVHASLDKFLANVSTVLTSKYR------ 141 HBA_ERIEU 111 HHPADFTPAVHASLDKFLATVATVLTSKYR------ 141 HBA_FRAPO 111 HHPSALTPEVHASLDKFLCAVGNVLTAKYR------ 141 HBA_PHACO 111 HHPSALTPEVHASLDKFLCAVGTVLTAKYR------ 141 HBA_TRIOC 111 HHPSVLTPEVHASLDKFLCAVGNVLSAKYR------ 141 HBA_ANSSE 111 HHPSLLTPEVHASMDKFLCAVATVLTAKYR------ 141 HBA_COLLI 111 HFPSLLTPEVHASLDKFVLAVGTVLTAKYR------ 141 HBAD_CHLM 111 HLGKDYSPEMHAAFDKFLSAVAAVLAEKYR------ 141 HBAD_PASM 111 RLGKEYSPEVHSAVDKFMSAVASVLAEKYR------ 141 HBAZ_HORS 111 RLPADFTADAHAAWDKFLSIVSSVLTEKYR------ 141 HBA4_SALI 112 YFPAEFTPEIHLSVDKFLQQLALALAEKYR------ 142 HBB_ORNAN 116 HFSKDFSPEVQAAWQKLVSGVAHALGHKYH------ 146 HBB_TACAC 116 HFSKEFTPEAQAAWQKLVSGVSHALAHKYH------ 146 HBE_PONPY 116 HFGKEFTPEVQAAWQKLVSAVAIALAHKYH------ 146 HBB_SPECI 116 HLGKDFTPEAQAAFQKVVAGVANALAHKYH------ 146 HBB_SPETO 116 HLGKDFTPEAQAAFQKVVAGVANALSHKYH------ 146 HBB_EQUHE 116 HFGKDFTPELQASYQKVVAGVANALAHKYH------ 146 HBB_SUNMU 116 KFGKEFTPPVQAAFQKVVAGVANALAHKYH------ 146 HBB_CALAR 116 HFGKEFTPVVQAAYQKVVAGVANALAHKYH------ 146 HBB_MANSP 116 HFGKEFTPQVQAAYQKVVAGVANALAHKYH------ 146 HBB_URSMA 116 HFGKEFTPQVQAAYQKVVAGVANALAHKYH------ 146 HBB_RABIT 116 HFGKEFTPQVQAAYQKVVAGVANALAHKYH------ 146 HBB_TUPGL 116 NFGPEFTPQVQAAFQKVVAGVANALAHKYH------ 146 HBB_TRIIN 116 HFGKEFSPEAQAAYQKVVAGVANALAHKYH------ 146 HBB_COLLI 116 HFGKDFTPECQAAWQKLVRVVAHALARKYH------ 146 HBB_LARRI 116 HFAKDFTPDSQAAWQKLVRVVAHALARKYH------ 146 HBB1_VARE 116 HHGKEFTPAHHAAYQKLVNVVSHSLARRYH------ 146 HBB2_XENT 116 KLGSAFTPQVQAVWEKLNATLVAALSHGY-f----- 146 HBBL_RANC 116 KLGKAFSPQVQHVWEKFIAVLVDALSHSYH------ 146 HBB2_TRIC 116 TLQTDFSCHKQLAFEKLMKGVSHALGHGY------- 145 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF SQ 45 MYG_ESCGI .-VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKelgfqg #=GR MYG_ESCGI PP ..69****************************************************************************.99******************************************************************7****** MYG_HORSE g--LSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKelgfqg #=GR MYG_HORSE PP 8..89***************************************************************************.99******************************************************************7****** MYG_PROGU g--LSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLKAEDEMRASEELKKHGTTVLTALGGILKK-KGQHAAELAPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKelgfqg #=GR MYG_PROGU PP 8..89***************************************************************************.99******************************************************************7****** MYG_SAISC g--LSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASEELKKHGTTVLTALGGILKK-KGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKelgfqg #=GR MYG_SAISC PP 8..89***************************************************************************.99******************************************************************7****** MYG_LYCPI g--LSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKelgfqg #=GR MYG_LYCPI PP 8..89***************************************************************************.99******************************************************************7****** MYG_MOUSE g--LSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSEDLKKHGCTVLTALGTILKK-KGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKelgfqg #=GR MYG_MOUSE PP 8..89***************************************************************************.99******************************************************************7****** MYG_MUSAN v------DWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQADTVLSALGNIVKK-KGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKaanfqg #=GR MYG_MUSAN PP 7......89***************************************9877.89*************************.99****************************************************************997****** HBA_AILME .-VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTTAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR...... #=GR HBA_AILME PP ..69********************************************.9**.....9***********************9.******************************************************************7...... HBA_PROLO .-VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTLAVGHLD-DLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR...... #=GR HBA_PROLO PP ..69********************************************.9**.....9***********************9.******************************************************************7...... HBA_PAGLA .-VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHF-DLS-----HGSAQVKAHGKKVADALTLAVGHLE-DLPNALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR...... #=GR HBA_PAGLA PP ..69********************************************.***.....***********************98.9*****************************************************************7...... HBA_MACFA .-VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... #=GR HBA_MACFA PP ..69********************************************.***.....************************9.******************************************************************7...... HBA_MACSI .-VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... #=GR HBA_MACSI PP ..69********************************************.***.....************************9.******************************************************************7...... HBA_PONPY .-VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKDHGKKVADALTNAVAHVD-DMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... #=GR HBA_PONPY PP ..69********************************************.***.....************************9.******************************************************************7...... HBA2_GALCR .-VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSTQVKGHGKKVADALTNAVLHVD-DMPSALSALSDLHAHKLRVDPVNFKLLRHCLLVTLACHHPAEFTPAVHASLDKFMASVSTVLTSKYR...... #=GR HBA2_GALCR PP ..69********************************************.***.....************************9.******************************************************************7...... HBA_MESAU .-VLSAKDKTNISEAWGKIGGHAGEYGAEALERMFFVYPTTKTYFPHF-DVS-----HGSAQVKGHGKKVADALTNAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPADFTPAVHASLDKFFASVSTVLTSKYR...... #=GR HBA_MESAU PP ..69********************************************.888.....************************9.******************************************************************7...... HBA2_BOSMU .-VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGAKVAAALTKAVGHLD-DLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR...... #=GR HBA2_BOSMU PP ..69********************************************.***.....************************9.******************************************************************7...... HBA_ERIEU .-VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHF-DLN-----PGSAQVKGHGKKVADALTTAVNNLD-DVPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLALHHPADFTPAVHASLDKFLATVATVLTSKYR...... #=GR HBA_ERIEU PP ..69********************************************.999.....9***********************9.9*****************************************************************7...... HBA_FRAPO .-VLSAADKNNVKGIFGKISSHAEDYGAEALERMFITYPSTKTYFPHF-DLS-----HGSAQVKGHGKKVVAALIEAANHID-DIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGNVLTAKYR...... #=GR HBA_FRAPO PP ..69********************************************.***.....************************9.9*****************************************************************7...... HBA_PHACO .-VLSAADKNNVKGIFTKIAGHAEEYGAEALERMFITYPSTKTYFPHF-DLS-----HGSAQIKGHGKKVVAALIEAVNHID-DITGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGTVLTAKYR...... #=GR HBA_PHACO PP ..69********************************************.***.....************************9.9*****************************************************************7...... HBA_TRIOC .-VLSANDKTNVKTVFTKITGHAEDYGAETLERMFITYPPTKTYFPHF-DLH-----HGSAQIKAHGKKVVGALIEAVNHID-DIAGALSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPSVLTPEVHASLDKFLCAVGNVLSAKYR...... #=GR HBA_TRIOC PP ..69********************************************.999.....************************9.9*****************************************************************7...... HBA_ANSSE .-VLSAADKGNVKTVFGKIGGHAEEYGAETLQRMFQTFPQTKTYFPHF-DLQ-----PGSAQIKAHGKKVAAALVEAANHID-DIAGALSKLSDLHAQKLRVDPVNFKFLGHCFLVVLAIHHPSLLTPEVHASMDKFLCAVATVLTAKYR...... #=GR HBA_ANSSE PP ..69********************************************.999.....9***********************9.9*****************************************************************7...... HBA_COLLI .-VLSANDKSNVKAVFAKIGGQAGDLGGEALERLFITYPQTKTYFPHF-DLS-----HGSAQIKGHGKKVAEALVEAANHID-DIAGALSKLSDLHAQKLRVDPVNFKLLGHCFLVVVAVHFPSLLTPEVHASLDKFVLAVGTVLTAKYR...... #=GR HBA_COLLI PP ..69********************************************.***.....************************9.9*****************************************************************7...... HBAD_CHLME m--LTADDKKLLTQLWEKVAGHQEEFGSEALQRMFLTYPQTKTYFPHF-DLH-----PGSEQVRGHGKKVAAALGNAVKSLD-NLSQALSELSNLHAYNLRVDPANFKLLAQCFQVVLATHLGKDYSPEMHAAFDKFLSAVAAVLAEKYR...... #=GR HBAD_CHLME PP 6..89*******************************************.999.....9************************.******************************************************************7...... HBAD_PASMO m--LTAEDKKLIQQIWGKLGGAEEEIGADALWRMFHSYPSTKTYFPHF-DLS-----QGSDQIRGHGKKVVAALSNAIKNLD-NLSQALSELSNLHAYNLRVDPVNFKFLSQCLQVSLATRLGKEYSPEVHSAVDKFMSAVASVLAEKYR...... #=GR HBAD_PASMO PP 6..99*******************************************.9**.....9************************.******************************************************************7...... HBAZ_HORSE s--LTKAERTMVVSIWGKISMQADAVGTEALQRLFSSYPQTKTYFPHF-DLH-----EGSPQLRAHGSKVAAAVGDAVKSID-NVAGALAKLSELHAYILRVDPVNFKFLSHCLLVTLASRLPADFTADAHAAWDKFLSIVSSVLTEKYR...... #=GR HBAZ_HORSE PP 6..89*******************************************.999.....9************************.******************************************************************7...... HBA4_SALIR s--LSAKDKANVKAIWGKILPKSDEIGEQALSRMLVVYPQTKAYFSHWASVA-----PGSAPVKKHGITIMNQIDDCVGHMD-DLFGFLTKLSELHATKLRVDPTNFKILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR...... #=GR HBA4_SALIR PP 6..9********************************************7776.....9************************.9*****************************************************************7...... HBB_ORNAN .VHLSGGEKSAVTNLWGKV--NINELGGEALGRLLVVYPWTQRFFEAFGDLSSAGAVMGNPKVKAHGAKVLTSFGDALKNLD-DLKGTFAKLSELHCDKLHVDPENFNRLGNVLIVVLARHFSKDFSPEVQAAWQKLVSGVAHALGHKYH...... #=GR HBB_ORNAN PP .69****************..************************************************************9.******************************************************************7...... HBB_TACAC .VHLSGSEKTAVTNLWGHV--NVNELGGEALGRLLVVYPWTQRFFESFGDLSSADAVMGNAKVKAHGAKVLTSFGDALKNLD-NLKGTFAKLSELHCDKLHVDPENFNRLGNVLVVVLARHFSKEFTPEAQAAWQKLVSGVSHALAHKYH...... #=GR HBB_TACAC PP .69****************..*************************************************************.******************************************************************7...... HBE_PONPY .VHFTAEEKAAVTSLWSKM--NVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNMD-NLKTTFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH...... #=GR HBE_PONPY PP .5789**************..*************************************************************.******************************************************************7...... HBB_SPECI .VHLSDGEKNAISTAWGKV--HAAEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLD-NLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALAHKYH...... #=GR HBB_SPECI PP .69****************..99***********************************************************.******************************************************************7...... HBB_SPETO .VHLTDGEKNAISTAWGKV--NAAEIGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLD-NLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALSHKYH...... #=GR HBB_SPETO PP .69****************..99***********************************************************.******************************************************************7...... HBB_EQUHE v-QLSGEEKAAVLALWDKV--NEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPAAVMGNPKVKAHGKKVLHSFGEGVHHLD-NLKGTFAQLSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH...... #=GR HBB_EQUHE PP 5.79***************..99***********************************************************.******************************************************************7...... HBB_SUNMU .VHLSGEEKACVTGLWGKV--NEDEVGAEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNPKVKAHGKKVLHSLGEGVANLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVVVLASKFGKEFTPPVQAAFQKVVAGVANALAHKYH...... #=GR HBB_SUNMU PP .69****************..99***********************************************************.******************************************************************7...... HBB_CALAR .VHLTGEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMNNPKVKAHGKKVLGAFSDGLTHLD-NLKGTFAHLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPVVQAAYQKVVAGVANALAHKYH...... #=GR HBB_CALAR PP .689***************..*************************************************************.******************************************************************7...... HBB_MANSP .VHLTPEEKTAVTTLWGKV--NVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPDAVMGNPKVKAHGKKVLGAFSDGLNHLD-NLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... #=GR HBB_MANSP PP .69****************..*************************************************************.******************************************************************7...... HBB_URSMA .VHLTGEEKSLVTGLWGKV--NVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSADAIMNNPKVKAHGKKVLNSFSDGLKNLD-NLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... #=GR HBB_URSMA PP .689***************..*************************************************************.******************************************************************7...... HBB_RABIT .VHLSSEEKSAVTALWGKV--NVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... #=GR HBB_RABIT PP .69****************..*************************************************************.******************************************************************7...... HBB_TUPGL .VHLSGEEKAAVTGLWGKV--DLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH...... #=GR HBB_TUPGL PP .69****************..*************************************************************.******************************************************************7...... HBB_TRIIN .VHLTPEEKALVIGLWAKV--NVKEYGGEALGRLLVVYPWTQRFFEHFGDLSSASAIMNNPKVKAHGEKVFTSFGDGLKHLE-DLKGAFAELSELHCDKLHVDPENFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH...... #=GR HBB_TRIIN PP .69****************..***********************************************************98.9*****************************************************************7...... HBB_COLLI v-HWSAEEKQLITSIWGKV--NVADCGAEALARLLIVYPWTQRFFSSFGNLSSATAISGNPNVKAHGKKVLTSFGDAVKNLD-NIKGTFAQLSELHCDKLHVDPENFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH...... #=GR HBB_COLLI PP 5.779**************..*************************************************************.******************************************************************7...... HBB_LARRI v-HWSAEEKQLITGLWGKV--NVADCGAEALARLLIVYPWTQRFFASFGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLD-NIKNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH...... #=GR HBB_LARRI PP 5.779**************..*************************************************************.******************************************************************7...... HBB1_VAREX v-HWTAEEKQLICSLWGKI--DVGLIGGETLAGLLVIYPWTQRQFSHFGNLSSPTAIAGNPRVKAHGKKVLTSFGDAIKNLD-NIKDTFAKLSELHCDKLHVDPTNFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH...... #=GR HBB1_VAREX PP 6.6799*************..*************************************************************.******************************************************************7...... HBB2_XENTR v-HWTAEEKATIASVWGKV--DIEQDGHDALSRLLVVYPWTQRYFSSFGNLSNVSAVSGNVKVKAHGNKVLSAVGSAIQHLD-DVKSHLKGLSKSHAEDLHVDPENFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGY-f..... #=GR HBB2_XENTR PP 6.6799*************..************************************************************9.9*************************************************************9988.9..... HBBL_RANCA v-HWTAEEKAVINSVWQKV--DVEQDGHEALTRLFIVYPWTQRYFSTFGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLD-DVKGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH...... #=GR HBBL_RANCA PP 6.6799*************..************************************************************9.9*****************************************************************7...... HBB2_TRICR .VHLTAEDRKEIAAILGKV--NVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLD-NLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY-...... #=GR HBB2_TRICR PP .69****************..*************************************************************.**************************************************************9988....... #=GC PP_cons .679*****************************************************************************99******************************************************************7...... #=GC RF .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... // """, ) def check_alignment_pfam1(self, alignment): """Check the alignment obtained by parsing Pfam record 120_Rick_ant.""" self.assertEqual(alignment.annotations["identifier"], "120_Rick_ant") self.assertEqual(alignment.annotations["accession"], "PF12574.10") self.assertEqual( alignment.annotations["definition"], "120 KDa Rickettsia surface antigen" ) self.assertEqual(alignment.annotations["author"], ["Gavin OL;"]) self.assertEqual(alignment.annotations["source of seed"], "Prosite") self.assertEqual(alignment.annotations["gathering method"], "25.00 25.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "42.00 39.60;") self.assertEqual(alignment.annotations["noise cutoff"], "23.60 21.20;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "8112862") self.assertEqual( alignment.annotations["references"][0]["title"], "Cloning, sequencing, and expression of the gene coding for an antigenic 120-kilodalton protein of Rickettsia conorii.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Schuenke KW, Walker DH;" ) self.assertEqual( alignment.annotations["references"][0]["location"], "Infect Immun. 1994;62:904-909.", ) self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0], {"reference": "INTERPRO; IPR020954;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "SO; 0100021; polypeptide_conserved_region;"}, ) self.assertEqual( alignment.annotations["comment"], "This domain family is found in bacteria, and is approximately 40 amino acids in length. This family is a Rickettsia surface antigen of 120 KDa which may be used as an antigen for immune response against the bacterial species.", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 8, 8, 229, 231, 235], [0, 8, 13, 234, 234, 238]]), ) ) self.assertEqual(alignment.sequences[0].id, "SCA4_RICPR/103-337") self.assertEqual( alignment.sequences[0].seq, "LAEQIAKEEDDRKFRAFLSNQDNYALINKAFEDTKTKKNLEKAEIVGYKNVLSTYSVANGYQGGFQPVQWENQVSASDLRSTVVKNDEGEELCTLNETTVKTKDLIVAKQDGTQVQINSYREINFPIKLDKANGSMHLSMVALKADGTKPAKDKAVYFTAHYEEGPNGKPQLKEISSPQPLKFVGTGDDAVAYIEHGGEIYTLAVTRGKYKEMMKEVALNHGQSVALSQTIAEDL", ) self.assertEqual(alignment.sequences[0].annotations["accession"], "Q9ZD49.2") self.assertEqual(alignment.sequences[1].id, "H8K5G2_RICAG/113-350") self.assertEqual( alignment.sequences[1].seq, "LAEQKRKEIEEEKEKDKTLSTFFGNPANREFIDKALENPELKKKLESIEIAGYKNVHNTFSAASGYPGGFKPVQWENQVSANDLRATVVKNDAGDELCTLNETTVKTKPFTVAKQDGTQVQISSYREIDFPIKLDKADGSMHLSMVALKADGTKPSKDKAVYFTAHYEEGPNGKPQLKEISSPKPLKFAGTGDDAIAYIEHGGEIYTLAVTRGKYKEMMKEVELNQGQSVDLSQAEDI", ) self.assertEqual(alignment.sequences[1].annotations["accession"], "H8K5G2.1") self.assertEqual( alignment[0], "LAEQIAKE-----EDDRKFRAFLSNQDNYALINKAFEDTKTKKNLEKAEIVGYKNVLSTYSVANGYQGGFQPVQWENQVSASDLRSTVVKNDEGEELCTLNETTVKTKDLIVAKQDGTQVQINSYREINFPIKLDKANGSMHLSMVALKADGTKPAKDKAVYFTAHYEEGPNGKPQLKEISSPQPLKFVGTGDDAVAYIEHGGEIYTLAVTRGKYKEMMKEVALNHGQSVALSQTIAEDL", ) self.assertEqual( alignment[1], "LAEQKRKEIEEEKEKDKTLSTFFGNPANREFIDKALENPELKKKLESIEIAGYKNVHNTFSAASGYPGGFKPVQWENQVSANDLRATVVKNDAGDELCTLNETTVKTKPFTVAKQDGTQVQISSYREIDFPIKLDKADGSMHLSMVALKADGTKPSKDKAVYFTAHYEEGPNGKPQLKEISSPKPLKFAGTGDDAIAYIEHGGEIYTLAVTRGKYKEMMKEVELNQGQSVDLSQ--AEDI", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "LAEQhtKE.....EcD+phpsFhuN.sNhthIsKAhEsschKKpLEphEIsGYKNVhsTaSsAsGY.GGFpPVQWENQVSAsDLRuTVVKNDtG-ELCTLNETTVKTKshhVAKQDGTQVQIsSYREIsFPIKLDKAsGSMHLSMVALKADGTKPuKDKAVYFTAHYEEGPNGKPQLKEISSPpPLKFsGTGDDAlAYIEHGGEIYTLAVTRGKYKEMMKEVtLNpGQSVsLSQ..AEDl", ) self.assertEqual( str(alignment), """\ SCA4_RICP 0 LAEQIAKE-----EDDRKFRAFLSNQDNYALINKAFEDTKTKKNLEKAEIVGYKNVLSTY 0 ||||..||-----|.|.....|..|..|...|.||.|....||.||..||.|||||..|. H8K5G2_RI 0 LAEQKRKEIEEEKEKDKTLSTFFGNPANREFIDKALENPELKKKLESIEIAGYKNVHNTF SCA4_RICP 55 SVANGYQGGFQPVQWENQVSASDLRSTVVKNDEGEELCTLNETTVKTKDLIVAKQDGTQV 60 |.|.||.|||.||||||||||.|||.||||||.|.|||||||||||||...||||||||| H8K5G2_RI 60 SAASGYPGGFKPVQWENQVSANDLRATVVKNDAGDELCTLNETTVKTKPFTVAKQDGTQV SCA4_RICP 115 QINSYREINFPIKLDKANGSMHLSMVALKADGTKPAKDKAVYFTAHYEEGPNGKPQLKEI 120 ||.|||||.||||||||.|||||||||||||||||.|||||||||||||||||||||||| H8K5G2_RI 120 QISSYREIDFPIKLDKADGSMHLSMVALKADGTKPSKDKAVYFTAHYEEGPNGKPQLKEI SCA4_RICP 175 SSPQPLKFVGTGDDAVAYIEHGGEIYTLAVTRGKYKEMMKEVALNHGQSVALSQTIAEDL 180 |||.||||.||||||.||||||||||||||||||||||||||.||.||||.|||--|||. H8K5G2_RI 180 SSPKPLKFAGTGDDAIAYIEHGGEIYTLAVTRGKYKEMMKEVELNQGQSVDLSQ--AEDI SCA4_RICP 235 240 H8K5G2_RI 238 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 120_Rick_ant #=GF AC PF12574.10 #=GF DE 120 KDa Rickettsia surface antigen #=GF AU Gavin OL; #=GF SE Prosite #=GF GA 25.00 25.00; #=GF TC 42.00 39.60; #=GF NC 23.60 21.20; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF RN [1] #=GF RM 8112862 #=GF RT Cloning, sequencing, and expression of the gene coding for an #=GF RT antigenic 120-kilodalton protein of Rickettsia conorii. #=GF RA Schuenke KW, Walker DH; #=GF RL Infect Immun. 1994;62:904-909. #=GF DR INTERPRO; IPR020954; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC This domain family is found in bacteria, and is approximately 40 #=GF CC amino acids in length. This family is a Rickettsia surface antigen of #=GF CC 120 KDa which may be used as an antigen for immune response against #=GF CC the bacterial species. #=GF SQ 2 #=GS SCA4_RICPR/103-337 AC Q9ZD49.2 #=GS H8K5G2_RICAG/113-350 AC H8K5G2.1 SCA4_RICPR/103-337 LAEQIAKE.....EDDRKFRAFLSNQDNYALINKAFEDTKTKKNLEKAEIVGYKNVLSTYSVANGYQGGFQPVQWENQVSASDLRSTVVKNDEGEELCTLNETTVKTKDLIVAKQDGTQVQINSYREINFPIKLDKANGSMHLSMVALKADGTKPAKDKAVYFTAHYEEGPNGKPQLKEISSPQPLKFVGTGDDAVAYIEHGGEIYTLAVTRGKYKEMMKEVALNHGQSVALSQTIAEDL H8K5G2_RICAG/113-350 LAEQKRKEIEEEKEKDKTLSTFFGNPANREFIDKALENPELKKKLESIEIAGYKNVHNTFSAASGYPGGFKPVQWENQVSANDLRATVVKNDAGDELCTLNETTVKTKPFTVAKQDGTQVQISSYREIDFPIKLDKADGSMHLSMVALKADGTKPSKDKAVYFTAHYEEGPNGKPQLKEISSPKPLKFAGTGDDAIAYIEHGGEIYTLAVTRGKYKEMMKEVELNQGQSVDLSQ..AEDI #=GC seq_cons LAEQhtKE.....EcD+phpsFhuN.sNhthIsKAhEsschKKpLEphEIsGYKNVhsTaSsAsGY.GGFpPVQWENQVSAsDLRuTVVKNDtG-ELCTLNETTVKTKshhVAKQDGTQVQIsSYREIsFPIKLDKAsGSMHLSMVALKADGTKPuKDKAVYFTAHYEEGPNGKPQLKEISSPpPLKFsGTGDDAlAYIEHGGEIYTLAVTRGKYKEMMKEVtLNpGQSVsLSQ..AEDl // """, ) def check_alignment_pfam2(self, alignment): """Check the alignment obtained by parsing Pfam record 7kD_DNA_binding.""" self.assertEqual(alignment.annotations["identifier"], "7kD_DNA_binding") self.assertEqual(alignment.annotations["accession"], "PF02294.20") self.assertEqual(alignment.annotations["definition"], "7kD DNA-binding domain") self.assertEqual(len(alignment.annotations["author"]), 2) self.assertEqual( alignment.annotations["author"][0], "Mian N;0000-0003-4284-4749" ) self.assertEqual( alignment.annotations["author"][1], "Bateman A;0000-0002-6982-4660" ) self.assertEqual( alignment.annotations["source of seed"], "Pfam-B_8148 (release 5.2)" ) self.assertEqual(alignment.annotations["gathering method"], "25.00 25.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "26.60 46.20;") self.assertEqual(alignment.annotations["noise cutoff"], "23.20 19.20;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Domain") self.assertEqual(alignment.annotations["clan"], "CL0049") self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "3130377") self.assertEqual( alignment.annotations["references"][0]["title"], "Microsequence analysis of DNA-binding proteins 7a, 7b, and 7e from the archaebacterium Sulfolobus acidocaldarius.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Choli T, Wittmann-Liebold B, Reinhardt R;", ) self.assertEqual( alignment.annotations["references"][0]["location"], "J Biol Chem 1988;263:7087-7093.", ) self.assertEqual(len(alignment.annotations["database references"]), 3) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR003212;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "SCOP; 1sso; fa;", ) self.assertEqual( alignment.annotations["database references"][2]["reference"], "SO; 0000417; polypeptide_domain;", ) self.assertEqual( alignment.annotations["comment"], "This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.", ) self.assertEqual(alignment.sequences[0].id, "DN7_METS5/4-61") self.assertEqual(alignment.sequences[0].annotations["accession"], "A4YEA2.1") self.assertEqual(alignment.sequences[1].id, "DN7A_SACS2/3-61") self.assertEqual(alignment.sequences[1].annotations["accession"], "P61991.2") self.assertEqual(len(alignment.sequences[1].dbxrefs), 4) self.assertEqual(alignment.sequences[1].dbxrefs[0], "PDB; 1SSO A; 2-60;") self.assertEqual(alignment.sequences[1].dbxrefs[1], "PDB; 1JIC A; 2-60;") self.assertEqual(alignment.sequences[1].dbxrefs[2], "PDB; 2CVR A; 2-60;") self.assertEqual(alignment.sequences[1].dbxrefs[3], "PDB; 1B4O A; 2-60;") self.assertEqual(alignment.sequences[2].id, "DN7E_SULAC/3-60") self.assertEqual(alignment.sequences[2].annotations["accession"], "P13125.2") self.assertEqual( alignment.sequences[0].seq, "KIKFKYKGQDLEVDISKVKKVWKVGKMVSFTYDDNGKTGRGAVSEKDAPKELLNMIGK", ) self.assertEqual( alignment.sequences[1].seq, "TVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEK", ) self.assertEqual( alignment.sequences[2].seq, "KVRFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELMDMLAR", ) self.assertEqual( alignment[0], "KIKFKYKGQDLEVDISKVKKVWKVGKMVSFTYDD-NGKTGRGAVSEKDAPKELLNMIGK" ) self.assertEqual( alignment[1], "TVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEK" ) self.assertEqual( alignment[2], "KVRFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDD-NGKTGRGAVSEKDAPKELMDMLAR" ) self.assertEqual( alignment.sequences[1].letter_annotations["secondary structure"], "EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSSEEEEEEETTTS-CHHHHHHTT", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], "EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSSEEEEEEETTTS-CHHHHHHTT", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "KVKFKYKGEEKEVDISKIKKVWRVGKMVSFTYDD.NGKTGRGAVSEKDAPKELLsMLuK", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 34, 34, 58], [0, 34, 35, 59], [0, 34, 34, 58]]), ) ) self.assertEqual( str(alignment), """\ DN7_METS5 0 KIKFKYKGQDLEVDISKVKKVWKVGKMVSFTYDD-NGKTGRGAVSEKDAPKELLNMIGK DN7A_SACS 0 TVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEK DN7E_SULA 0 KVRFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDD-NGKTGRGAVSEKDAPKELMDMLAR DN7_METS5 58 DN7A_SACS 59 DN7E_SULA 58 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 7kD_DNA_binding #=GF AC PF02294.20 #=GF DE 7kD DNA-binding domain #=GF AU Mian N;0000-0003-4284-4749 #=GF AU Bateman A;0000-0002-6982-4660 #=GF SE Pfam-B_8148 (release 5.2) #=GF GA 25.00 25.00; #=GF TC 26.60 46.20; #=GF NC 23.20 19.20; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF CL CL0049 #=GF RN [1] #=GF RM 3130377 #=GF RT Microsequence analysis of DNA-binding proteins 7a, 7b, and 7e from #=GF RT the archaebacterium Sulfolobus acidocaldarius. #=GF RA Choli T, Wittmann-Liebold B, Reinhardt R; #=GF RL J Biol Chem 1988;263:7087-7093. #=GF DR INTERPRO; IPR003212; #=GF DR SCOP; 1sso; fa; #=GF DR SO; 0000417; polypeptide_domain; #=GF CC This family contains members of the hyper-thermophilic #=GF CC archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There #=GF CC are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the #=GF CC cell. Protein 7e shows the tightest DNA-binding ability. #=GF SQ 3 #=GS DN7_METS5/4-61 AC A4YEA2.1 #=GS DN7A_SACS2/3-61 AC P61991.2 #=GS DN7A_SACS2/3-61 DR PDB; 1SSO A; 2-60; #=GS DN7A_SACS2/3-61 DR PDB; 1JIC A; 2-60; #=GS DN7A_SACS2/3-61 DR PDB; 2CVR A; 2-60; #=GS DN7A_SACS2/3-61 DR PDB; 1B4O A; 2-60; #=GS DN7E_SULAC/3-60 AC P13125.2 DN7_METS5/4-61 KIKFKYKGQDLEVDISKVKKVWKVGKMVSFTYDD.NGKTGRGAVSEKDAPKELLNMIGK DN7A_SACS2/3-61 TVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEK #=GR DN7A_SACS2/3-61 SS EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSSEEEEEEETTTS-CHHHHHHTT DN7E_SULAC/3-60 KVRFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDD.NGKTGRGAVSEKDAPKELMDMLAR #=GC SS_cons EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSSEEEEEEETTTS-CHHHHHHTT #=GC seq_cons KVKFKYKGEEKEVDISKIKKVWRVGKMVSFTYDD.NGKTGRGAVSEKDAPKELLsMLuK // """, ) def check_alignment_pfam3(self, alignment): """Check the alignment obtained by parsing Pfam record 12TM_1.""" self.assertEqual(alignment.annotations["identifier"], "12TM_1") self.assertEqual(alignment.annotations["accession"], "PF09847.11") self.assertEqual( alignment.annotations["definition"], "Membrane protein of 12 TMs" ) self.assertEqual(alignment.annotations["previous identifier"], "DUF2074;") self.assertEqual(len(alignment.annotations["author"]), 3) self.assertEqual(alignment.annotations["author"][0], "COGs;") self.assertEqual( alignment.annotations["author"][1], "Finn RD;0000-0001-8626-2148" ) self.assertEqual( alignment.annotations["author"][2], "Sammut SJ;0000-0003-4472-904X" ) self.assertEqual(alignment.annotations["source of seed"], "COGs (COG3368)") self.assertEqual(alignment.annotations["gathering method"], "33.20 33.20;") self.assertEqual(alignment.annotations["trusted cutoff"], "33.60 33.20;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["noise cutoff"], "33.10 32.90;") self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual(alignment.annotations["clan"], "CL0181") self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR018646;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "SO; 0100021; polypeptide_conserved_region;", ) self.assertEqual( alignment.annotations["comment"], "This family carries twelve transmembrane regions. It does not have any characteristic nucleotide-binding-domains of the GxSGSGKST type. so it may not be an ATP-binding cassette transporter. However, it may well be a transporter of some description. ABC transporters always have two nucleotide binding domains; this has two unusual conserved sequence-motifs: 'KDhKxhhR' and 'LxxLP'.", ) self.assertEqual(alignment.sequences[0].id, "O29855_ARCFU/39-477") self.assertEqual(alignment.sequences[1].id, "O29125_ARCFU/30-435") self.assertEqual(alignment.sequences[2].id, "Q8U2D3_PYRFU/39-485") self.assertEqual(alignment.sequences[3].id, "Q5JDA6_THEKO/35-482") self.assertEqual(alignment.sequences[4].id, "Q97VM1_SACS2/39-451") self.assertEqual(alignment.sequences[5].id, "Q9HM06_THEAC/17-497") self.assertEqual(alignment.sequences[6].id, "Q6L2L5_PICTO/38-510") self.assertEqual(alignment.sequences[0].annotations["accession"], "O29855.1") self.assertEqual(alignment.sequences[1].annotations["accession"], "O29125.1") self.assertEqual(alignment.sequences[2].annotations["accession"], "Q8U2D3.1") self.assertEqual(alignment.sequences[3].annotations["accession"], "Q5JDA6.1") self.assertEqual(alignment.sequences[4].annotations["accession"], "Q97VM1.1") self.assertEqual(alignment.sequences[5].annotations["accession"], "Q9HM06.1") self.assertEqual(alignment.sequences[6].annotations["accession"], "Q6L2L5.1") self.assertEqual( alignment.sequences[0].seq, "WIRYNALLLKIMFTFAALFSVGPAFFDDKVSYASSLLSLFFFFLMFGTAYAHGYFQVDLSYMHTFYSRSDISKVRFYGFFRLFDWPAVIALLSLLVLVGMRNPAGLLPALLGFLAVIMGALSIVILLGKRLGSVQTGRSLRAAFFRIFGLIAWLVSIYGLYLINQLAIYLMTFKNYEAYDSLFPISYGLWISQPFSAKYAALSLFYFALITLLFFYAVRELSKEEIAKHYGSLKGWKIKRRGKMTAMVIKDFKQLFRNPQLFVIALLPIYGALMQLVFYIKLSEVASVLYLQIFLAITVSSFMSLERSSYITALPLTDLEMKFSKILEGLLIYFVSMGIVAAVVIYKGGNLINSLSLFPTGFAVVLVAVQFSRRLTSEPVNVEAVIATLISFFIVLVPAAVGGVAVLILKAPFSSYAFPVSLAETLAVLAVFALLNRRK", ) self.assertEqual( alignment.sequences[1].seq, "SLRVQVAKSFFIMTFLGSFLCWVAFISSGLGLSLIFTLSLVFSQIYPAQNIAISASSRVFEPLRYLPVRFSERMLVVFFIDSINILAFATPTIAVLMVKNLYFGLYSLLWIIAAILLGYSMVFLYYALFGVKVRSGFSKSVLAGILFFAVLVFALRRFQEIPDLTPYLTPHLLLLSYAASSATIKLSTGRVWRSILNPEIVEVKGSSRLSSGSPLRAMLIKDFRLILRKNALFPLIVPLVIVMPNVVSIANMPNLSIFIITTISTLSTIDLRIIGNLENVDFLRMLPLSKRGFVMSKACLIFVISFAASLPAGSIAFIVSQNPFYLFMAFAIPAIVSMLSSLIIFWQKGEEIYFPEVGFLKWIGLLLVNFGAVYAVLSPRFILSQPVADIISSVLTLLAMTALFEK", ) self.assertEqual( alignment.sequences[2].seq, "NIIWGVFLQSVMYLGLGVMVAVSILYSENEVQKAIFFSSYLIIPFILTLYSTSLATAYLLSSKAVEPLKPLPLGNLNFIVSLTLLIENLPAFVFLIPASLALGNSIASLLGLLWICSTILMGHSLALFLQIKFSGIHVGKGSVVKTLVKVAGFLIIAGIYFIVQALMRILEDNIEVIAPIFRKYFIAFPFAASTIYEPYKSLVLLALYTLPFLALYFYDLKRLGEVLEGIKTYGKVATKYKLTVANPVTAMFRKDYRIIFRKNPYLGTFLSPLLMSIYFIYNLAKEGFPVMMTLFSIMGISVLGLVMLDPAFAMDREVFPFLSSLPIKRREYLLGKMLTVSLSPLTFSAILVLLSCAFNGTEALLLIPFLASPFLTSSIGILYVKHKMGNERIELPVLKFYDGIVMLILSMIPFIIVAIPLFLLSVPKGYLVSGAIILVGALILSKL", ) self.assertEqual( alignment.sequences[3].seq, "DLKKTLLFQTAMYAVFGLMLFPSLKGERDAVLVMASTYAILPFIIAFYATVTNSSYIASLDLFKPLLPLPIKLGGRYMSVLLLLESLPVMAFMVPGAVRIGMVVSATSGLLVLLWSAVGLMLGHVFGLLVYYSFGKTSSGRFADLKSLAKALGVILIFGLFYGFSYFQDYVLQNYTSIKESLGGYEFIYPLSVLSVDRPSFSAPLAGIYIAILGVAYYVLISRLWVRISEGSYTSGRRRRAGGLGVYPPELALMVKDFKTALRNTPVLTGLLVPIVIPIINVAGIFSNPDIGAFGGRLATITFVAALGWVSAVSVETLTKIEVKSFELLLSLPLERGRFLRGKLLTMAAIPSAVGVLALLGLSLKGFSSPIYLPMAVLVPLATCGIALHVYYHGTEGLALPQGGILKSLAVWILNAVVVGIIAGSWYLSYPIALLLTAAIDALLLWSL", ) self.assertEqual( alignment.sequences[4].seq, "NAVTIKISNIIAYTIATIVSASISLINKDAPFSFIFLDLIILANIFTTGLNVIFFVTNYDLKTFLLSLPLSERDVNRAVFRGIFEFFYYGFLASIVIAPISTYMITSSVLQALMAELEIIFFFSLSFALVMLLGKRIRLGITSALFRIGTSLIWIVFIMLPYGLTFKYVTIPTYILPIFPFGFLNIEGLLISLLYTGLSVFFAYKQSLKFLSFRLNSQYSTKYSIKLRSPLITYLYKDIRGLLRVPQASFLLTIPVFALIFSFFAPVYAIFYTIFMITTSSIMLILLEASGMQLLLSLPAGLRSSYISKLLIILIIYLIDVLIFSFFNRASLSLIMLPSTITSVELSLFISYNNVIKGKGMRLADPLSFIIREIEINSIIGIASILTFFANIYYSLLFSVLSLIMINIVVYKK", ) self.assertEqual( alignment.sequences[5].seq, "YVNISYGATSFSFIVFSLILVAPSLMEHRIYTLSSVVLLLFVYSLFINISNSLLFFVSVNINHILDPLRILPVDFPDHVIAVSWFIYTGSSSLFAVLPAIFLAAFLLGDPYILVIGLIWSIFSVLLGYIIGSSIFVAFGSRISGKRTRSTNILRNVGRIVFLVFVFAIFEIILYNANIVNGIIPRLPYPYSYFIPIFNIQSTVFFFHGIYMQATGFIISMVYTALASFAFIYVNRKAFYRLLEPTARNQSRVKTQMKAEVRSRPFSFFSKDLKISSRKSQNLVLLIMPLFFVFPTIMSEVLYAPTSKADPIILYNAMVAFVIVTSSFYSILFLVIEGNGISFIKALPLDGNSIIRWKISAPTFIFAVISISTLAAISVKALMGAAFYIIIIVDMMLYFVSSTVYNMNRLYRKIPDTADTVNFYSFGGQIAFITTFAFTGLIVGSADIFSLFLQDLLRLNAYFFFLINTVIGIIVLLFMVFR", ) self.assertEqual( alignment.sequences[6].seq, "TILLYYISNSLSFLFFSIVLNGIYYVKGNTNDISSFGIILFMYIFVIGIYSSLTYINGISINNLLSPVRSLPIKVNTDVPFLSWFIYTGSSYIFIIIPSLLFYYFLVHNLNTIILGLIYAFAMLLFGFIITAIAFIYSSRKPRAHTSLNNFLRILLIFVFLGFFYLIIYDPNILRAYSIYISSLPVYIKYIAFPLNIDYAVYFHPDIIATFFEYLSSFIILLIFFFIYKKIRSRLFYSLEYSEEVKSTEVTRTKIKRDSISVSFIKKDIKITARKSQNLTYILMPIIFVLPFLFTIISSRQPFLSLMFSILSLSILISSFYPIFTLIIENNGILIINALPINRKDIAKYKAYFSMIFYSIIITVVSIIIMAYKNIFNLYYVFIIPDLILIFYTAMIINLNRLIKKIPKGASTINYYSFGVFPTIVLFIVSGIIFGLLISPGIIISEFLYHSIKMSFIFDIIPDLIIFLIMIKK", ) self.assertEqual( alignment[0], "WIRYNALLLKIMFTFAALFSVGPAFFDDKVS----YASSLLSLFFFFLMFGTAYAHGYFQVDL---SYMHTFYSRSDISKVRFYGFFRLFDWPAVIALLS-----LLVLVGMRNPAGLLPALLGFLAVIMGALSIVILLGKRLGSVQTGR-SLRAAFFRIFGLIAWLVSIYGLYLINQLAI------YLMTFKNYEAYDSLFP-------ISYGLWISQPFSAKYAALSLFYF-ALITLLFFYAVRELSKE----EIAKHYGSLK-GWKIKRRGKMTAMVIKDFKQLFRNPQLFVIALLPIYGALM------------------QLVFYIKLSEVASVLYLQIFLAITVSSFMSLERSSYITALPLTDLEMKFSKILEGLLIYF-VSMGIVAAVVIYKG-GNLINSLSLFPTGFAVVLVAVQFSRRL-------TSEPVNVE---AVIATLISFFIVLVPAAVGGVAVLILKAPFS---SYAFPVSLAETLAVLAVFALLNRRK", ) self.assertEqual( alignment[1], "SLRVQVAKSFFIMTFLGSFLCWVAFISSGLG-----LSLIFTLSLVFSQIYPAQNIAISASS----RVFEPLRYLPVRFSERMLVVF-FIDSINILAFAT---PTIAVLMVKNLYFGLYSLLWIIAAILLG-YSMVFLYYALFGVKV--RSGFSKSVL--AGILFFAVLVFAL---------------RRFQEIPDLTPYLTP----------------------HLLLLSY--AASSATIKLSTGRVWRSILNPEIVEVKGSSR----LSSGSPLRAMLIKDFRLILRKN-ALFPLIVPLVIVMPNVVSIANMPN--------LSIFIITTISTLSTIDLRIIGNLENVDF--------LRMLPLSKRGFVMSKACLIFVISFAASLPAGSIAFIVS--QNPFYLFMAFAIPAIVSMLSSLIIFWQ-------KGEEIYFPEV-GFLKWIGLLLVNFGAVYAVLSPRFILSQPVA------DIISSVLTL----LAMTALFEK", ) self.assertEqual( alignment[2], "NIIWGVFLQSVMYLGLGVMVAVSILYSENEVQKAIFFSSYLIIPFILTLYSTSLATAYLLSS----KAVEPLKPLPLGNLNFIVSLTLLIENLPAFVFLI-----PASLALGNSIASLLGLLWICSTILMG-HSLALFLQIKFSGIHVGKGSVVKTLVKVAGFLI----IAGIYFIVQALMRILEDNIEVIAPIFRKYFIAFP--------FAASTIYEPYKS--LVLLALYT-LPFLALYFYDLKRLGEVL---EGIKTYGKVATKYKLTVANPVTAMFRKDYRIIFRKNPYLGTFLSPLLMSIYFIYNLAKEGFPVM-----MTLFSIMGISVLGLVMLDPAFAMDREVF------PFLSSLPIKRREYLLGKMLTVSLSPLTFSAILVLLSCAFNG-TEALLLIPFLASPFLTSSIGILYVKHKM------GNERIELPVL-KFYDGIVMLILSMIPFIIVAIPLFLLSVPKG------YLVSGAIIL----VGALILSKL", ) self.assertEqual( alignment[3], "DLKKTLLFQTAMYAVFGLML-FPSLKGERDA-VLVMASTYAILPFIIAFYATVTNSSYIASL----DLFKPLLPLPIKLGGRYMSVLLLLESLPVMAFMV--PGAVRIGMVVSATSGLLVLLWSAVGLMLG-HVFGLLVYYSFGKTSSGRFADLKSLAKALGVIL----IFGLFYGFSYFQDYVLQNYTSIKESLGGYEFIYP--------LSVLSVDRPSFS--APLAGIYI-AILGVAYYVLISRLWVRI--SEGSYTSGRRRRAGGLGVYPPELALMVKDFKTALRNTPVLTGLLVPIVIPIINVAGIFSNPDIGAFGGRLATITFVAALGWVSAVSVETLTKIEVKSF------ELLLSLPLERGRFLRGKLLTMAAIPSAVGV-LALLGLSLKGFSSPIYLPMAVLVPLATCGIALHVYYH--------GTEGLALPQG-GILKSLAVWILNAVVVGIIAG-SWYLSYPIA------LLLTAA-------IDALLLWSL", ) self.assertEqual( alignment[4], "NAVTIKISNIIAYTIATIVSASISLINKDAP----FSFIFLDLIILANIFTTGLNVIFFVTNY---DLKTFLLSLPLSERDVNRAVFRGIFEFFYYGFLA--SIVIAPISTYMITSSVLQALMAELEIIFF-FSLSFALVMLLGKRI--RLGITSALFRIGTSLIWIVFIMLPYGL-----------TFKYVTIPTYILPIFP--------FGFLNIEG------LLISLLYTGLSVFFAYKQSLKFLSFRL--------NSQYSTKYSIKLRSPLITYLYKDIRGLLRVPQASFLLTIPVFALIFSFFAPV------------YAIFYTIFMITTSSIMLIL---LEASGM------QLLLSLPAGLRSSYISKLLIILIIYL-------IDVLIFSFFNRASLSLIMLPSTITSVELSLFISYNNVI-----KGKGMRLA---DPLSFIIREIEINSIIGIASILTFFANIYYS------LLFSVLSLI----MINIVVYKK", ) self.assertEqual( alignment[5], "YVNISYGATSFSFIVFSLILVAPSLMEHRIY----TLSSVVLLLFVYSLFINISNSLLFFVSVNINHILDPLRILPVDFPDHVIAVSWFIYTGSSSLFAVLPAIFLAAFLLGDPYILVIGLIWSIFSVLLG-YIIGSSIFVAFGSRISGKRTRSTNILRNVGRIVFLVFVFAIFEIILYNANIV---NGIIPRLPYPYSYFIPIFNIQSTVFFFHGIYMQATG--FIISMVYT-ALASFAFIYVNRKAFYRLLEP-TARNQSRVKTQMKAEVRSRPFSFFSKDLKISSRKSQNLVLLIMPLFFVFPTIMSEVLYAPTSKADPIILYNAMVAFVIVTSSFYSILFLVIEGNGI------SFIKALPLDGNSIIRWKISAPTFIFAVISISTLAAISVKAL-MGAAFYIIIIVDMMLYFVSSTVYNMNRLYRKIPDTADTVNFYSFGGQIAFITTFAFTGLIVGSADIFSLFLQDLLRLNAYFFFLINTVIGI----IVLLFMVFR", ) self.assertEqual( alignment[6], "TILLYYISNSLSFLFFSIVLNGIYYVKGNTN----DISSFGIILFMYIFVIGIYSSLTYINGISINNLLSPVRSLPIKVNTDVPFLSWFIYTGSSYIFIIIPSLLFYYFLVHNLNTIILGLIYAFAMLLFG-FIITAIAFI-----YSSRKPRAHTSLNNFLRILLIFVFLGFFYLIIYDPNILRAYSIYISSLPVYIKYIAFPLNIDYAVYFHPDIIATFFE--YLSSFIIL-LIFFFIYKKIRSRLFYSL--EYSEEVKSTEVTRTKIKRDSISVSFIKKDIKITARKSQNLTYILMPIIFVLPFLFTIISSRQPFLS----LMFSILSLSILISSFYPIFTLIIENNGI------LIINALPINRKDIAKYKAYFSMIFYSIIITVVSIIIMAYKN-IFNLYYVFIIPDLILIFYTAMIINLNRLIKKIPKGASTINYYSF-GVFPTIVLFIVSGIIFGLLISPGIIISEFLYHSIKMSFIFDIIPDL----IIFLIMIKK", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "slhhthhhpphhahhhulhlsssuhhscphs....hhSohhhL.Flhshahsshsshhhhss....clhcPLhsLPlp.tschhulhhhI.shsshsFhs....hltshhlhs.hsulLsLLauhhsllhG.aslshhlhhhhGthhsuRhuhspslh+.hGhllhhh.lhulahl..h.........hhh.pl.thh.hlhP........hhh.sI.t...t..hlluhlYh.hhhhhhahhshp+Lhhpl....h.cspuphppthplphtu..huhhhKDh+hhhRps.sLshllhPlhhsl..lhs.h............hhlhhlthh.shSslhl.hhhhlEssuh.......hlpuLPlscpphhhuKhhhhhlI.hhhuh.hshhshhhph.tpshhhlhhlssshhsshluhhhshpp.......su-slph..h.uhlshIshhllshlhhulssh.shhLs..hu......hlloss.hl....lhhLlhhc+", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[0, 20, 21, 31, 31, 31, 32, 58, 59, 59, 80, 81, 93, 93, 93, 93, 119, 120, 129, 134, 135, 137, 138, 138, 145, 147, 152, 156, 160, 163, 168, 168, 168, 169, 184, 184, 185, 193, 197, 199, 206, 207, 207, 224, 224, 224, 224, 225, 229, 234, 234, 237, 259, 260, 274, 274, 274, 274, 274, 274, 293, 296, 302, 308, 310, 334, 334, 337, 338, 340, 347, 348, 348, 374, 375, 375, 375, 375, 383, 383, 383, 404, 405, 414, 414, 417, 423, 426, 430, 439], [0, 20, 21, 31, 31, 31, 31, 57, 57, 57, 78, 78, 90, 90, 90, 92, 118, 118, 127, 132, 133, 133, 134, 135, 142, 142, 147, 151, 155, 155, 155, 155, 155, 155, 170, 170, 170, 170, 170, 170, 177, 177, 177, 194, 195, 197, 198, 199, 203, 208, 208, 208, 230, 230, 244, 250, 254, 254, 254, 254, 273, 276, 282, 282, 282, 306, 307, 310, 311, 313, 320, 320, 320, 346, 347, 347, 347, 347, 355, 357, 357, 378, 379, 388, 388, 388, 394, 397, 397, 406], [0, 20, 21, 31, 32, 35, 36, 62, 62, 62, 83, 84, 96, 96, 96, 96, 122, 122, 131, 136, 137, 139, 140, 141, 148, 150, 155, 155, 159, 162, 167, 170, 173, 174, 189, 189, 189, 197, 201, 201, 208, 209, 209, 226, 227, 227, 227, 228, 232, 237, 238, 241, 263, 264, 278, 284, 288, 291, 291, 291, 310, 313, 319, 319, 321, 345, 346, 349, 350, 352, 359, 360, 360, 386, 387, 388, 388, 388, 396, 398, 398, 419, 420, 429, 429, 429, 435, 438, 438, 447], [0, 20, 20, 30, 30, 33, 34, 60, 60, 60, 81, 82, 94, 94, 95, 97, 123, 123, 132, 137, 138, 140, 141, 142, 149, 151, 156, 156, 160, 163, 168, 171, 174, 175, 190, 190, 190, 198, 202, 202, 209, 210, 210, 227, 228, 228, 229, 230, 234, 239, 240, 243, 265, 266, 280, 286, 290, 293, 294, 298, 317, 320, 326, 326, 328, 352, 353, 356, 356, 358, 365, 366, 367, 393, 393, 393, 393, 393, 401, 403, 403, 424, 424, 433, 433, 433, 439, 439, 439, 448], [0, 20, 21, 31, 31 , 31, 32, 58, 59, 59, 80, 81, 93, 93, 94, 96, 122, 122, 131, 136, 137, 137, 138, 139, 146, 148, 153, 157, 161, 164, 164, 164, 164, 165, 180, 180, 180, 188, 188, 188, 195, 196, 197, 214, 215, 215, 215, 215, 215, 220, 221, 224, 246, 247, 261, 267, 267, 267, 267, 267, 286, 286, 292, 292, 294, 318, 318, 318, 318, 318, 325, 326, 327, 353, 354, 355, 356, 356, 364, 364, 364, 385, 386, 395, 395, 395, 401, 404, 404, 413], [0, 20, 21, 31, 31, 31, 32, 58, 59, 62, 83, 84, 96, 98, 99, 101, 127, 127, 136, 141, 142, 144, 145, 146, 153, 155, 160, 164, 168, 171, 176, 179, 179, 180, 195, 202, 203, 211, 215, 215, 222, 223, 223, 240, 241, 243, 244, 244, 248, 253, 254, 257, 279, 280, 294, 300, 304, 307, 308, 312, 331, 334, 340, 340, 342, 366, 367, 370, 371, 373, 380, 381, 381, 407, 408, 409, 410, 415, 423, 425, 426, 447, 448, 457, 460, 463, 469, 472, 472, 481], [0, 20, 21, 31, 31, 31, 32, 58, 59, 62, 83, 84, 96, 98, 99, 101, 127, 127, 136, 136, 137, 139, 140, 141, 148, 150, 155, 159, 163, 166, 171, 174, 177, 178, 193, 200, 201, 209, 213, 213, 220, 221, 221, 238, 239, 239, 240, 241, 245, 250, 251, 254, 276, 277, 291, 297, 301, 304, 305, 305, 324, 327, 333, 333, 335, 359, 360, 363, 364, 366, 373, 374, 374, 400, 401, 402, 403, 408, 416, 418, 418, 439, 440, 449, 452, 455, 461, 464, 464, 473], ] # fmt: on ), ) ) self.assertEqual( str(alignment), """\ O29855_AR 0 WIRYNALLLKIMFTFAALFSVGPAFFDDKVS----YASSLLSLFFFFLMFGTAYAHGYFQ O29125_AR 0 SLRVQVAKSFFIMTFLGSFLCWVAFISSGLG-----LSLIFTLSLVFSQIYPAQNIAISA Q8U2D3_PY 0 NIIWGVFLQSVMYLGLGVMVAVSILYSENEVQKAIFFSSYLIIPFILTLYSTSLATAYLL Q5JDA6_TH 0 DLKKTLLFQTAMYAVFGLML-FPSLKGERDA-VLVMASTYAILPFIIAFYATVTNSSYIA Q97VM1_SA 0 NAVTIKISNIIAYTIATIVSASISLINKDAP----FSFIFLDLIILANIFTTGLNVIFFV Q9HM06_TH 0 YVNISYGATSFSFIVFSLILVAPSLMEHRIY----TLSSVVLLLFVYSLFINISNSLLFF Q6L2L5_PI 0 TILLYYISNSLSFLFFSIVLNGIYYVKGNTN----DISSFGIILFMYIFVIGIYSSLTYI O29855_AR 56 VDL---SYMHTFYSRSDISKVRFYGFFRLFDWPAVIALLS-----LLVLVGMRNPAGLLP O29125_AR 55 SS----RVFEPLRYLPVRFSERMLVVF-FIDSINILAFAT---PTIAVLMVKNLYFGLYS Q8U2D3_PY 60 SS----KAVEPLKPLPLGNLNFIVSLTLLIENLPAFVFLI-----PASLALGNSIASLLG Q5JDA6_TH 58 SL----DLFKPLLPLPIKLGGRYMSVLLLLESLPVMAFMV--PGAVRIGMVVSATSGLLV Q97VM1_SA 56 TNY---DLKTFLLSLPLSERDVNRAVFRGIFEFFYYGFLA--SIVIAPISTYMITSSVLQ Q9HM06_TH 56 VSVNINHILDPLRILPVDFPDHVIAVSWFIYTGSSSLFAVLPAIFLAAFLLGDPYILVIG Q6L2L5_PI 56 NGISINNLLSPVRSLPIKVNTDVPFLSWFIYTGSSYIFIIIPSLLFYYFLVHNLNTIILG O29855_AR 108 ALLGFLAVIMGALSIVILLGKRLGSVQTGR-SLRAAFFRIFGLIAWLVSIYGLYLINQLA O29125_AR 107 LLWIIAAILLG-YSMVFLYYALFGVKV--RSGFSKSVL--AGILFFAVLVFAL------- Q8U2D3_PY 111 LLWICSTILMG-HSLALFLQIKFSGIHVGKGSVVKTLVKVAGFLI----IAGIYFIVQAL Q5JDA6_TH 112 LLWSAVGLMLG-HVFGLLVYYSFGKTSSGRFADLKSLAKALGVIL----IFGLFYGFSYF Q97VM1_SA 111 ALMAELEIIFF-FSLSFALVMLLGKRI--RLGITSALFRIGTSLIWIVFIMLPYGL---- Q9HM06_TH 116 LIWSIFSVLLG-YIIGSSIFVAFGSRISGKRTRSTNILRNVGRIVFLVFVFAIFEIILYN Q6L2L5_PI 116 LIYAFAMLLFG-FIITAIAFI-----YSSRKPRAHTSLNNFLRILLIFVFLGFFYLIIYD O29855_AR 167 I------YLMTFKNYEAYDSLFP-------ISYGLWISQPFSAKYAALSLFYF-ALITLL O29125_AR 155 --------RRFQEIPDLTPYLTP----------------------HLLLLSY--AASSAT Q8U2D3_PY 166 MRILEDNIEVIAPIFRKYFIAFP--------FAASTIYEPYKS--LVLLALYT-LPFLAL Q5JDA6_TH 167 QDYVLQNYTSIKESLGGYEFIYP--------LSVLSVDRPSFS--APLAGIYI-AILGVA Q97VM1_SA 164 -------TFKYVTIPTYILPIFP--------FGFLNIEG------LLISLLYTGLSVFFA Q9HM06_TH 175 ANIV---NGIIPRLPYPYSYFIPIFNIQSTVFFFHGIYMQATG--FIISMVYT-ALASFA Q6L2L5_PI 170 PNILRAYSIYISSLPVYIKYIAFPLNIDYAVYFHPDIIATFFE--YLSSFIIL-LIFFFI O29855_AR 213 FFYAVRELSKE----EIAKHYGSLK-GWKIKRRGKMTAMVIKDFKQLFRNPQLFVIALLP O29125_AR 183 IKLSTGRVWRSILNPEIVEVKGSSR----LSSGSPLRAMLIKDFRLILRKN-ALFPLIVP Q8U2D3_PY 215 YFYDLKRLGEVL---EGIKTYGKVATKYKLTVANPVTAMFRKDYRIIFRKNPYLGTFLSP Q5JDA6_TH 216 YYVLISRLWVRI--SEGSYTSGRRRRAGGLGVYPPELALMVKDFKTALRNTPVLTGLLVP Q97VM1_SA 203 YKQSLKFLSFRL--------NSQYSTKYSIKLRSPLITYLYKDIRGLLRVPQASFLLTIP Q9HM06_TH 229 FIYVNRKAFYRLLEP-TARNQSRVKTQMKAEVRSRPFSFFSKDLKISSRKSQNLVLLIMP Q6L2L5_PI 227 YKKIRSRLFYSL--EYSEEVKSTEVTRTKIKRDSISVSFIKKDIKITARKSQNLTYILMP O29855_AR 268 IYGALM------------------QLVFYIKLSEVASVLYLQIFLAITVSSFMSLERSSY O29125_AR 238 LVIVMPNVVSIANMPN--------LSIFIITTISTLSTIDLRIIGNLENVDF-------- Q8U2D3_PY 272 LLMSIYFIYNLAKEGFPVM-----MTLFSIMGISVLGLVMLDPAFAMDREVF------PF Q5JDA6_TH 274 IVIPIINVAGIFSNPDIGAFGGRLATITFVAALGWVSAVSVETLTKIEVKSF------EL Q97VM1_SA 255 VFALIFSFFAPV------------YAIFYTIFMITTSSIMLIL---LEASGM------QL Q9HM06_TH 288 LFFVFPTIMSEVLYAPTSKADPIILYNAMVAFVIVTSSFYSILFLVIEGNGI------SF Q6L2L5_PI 285 IIFVLPFLFTIISSRQPFLS----LMFSILSLSILISSFYPIFTLIIENNGI------LI O29855_AR 310 ITALPLTDLEMKFSKILEGLLIYF-VSMGIVAAVVIYKG-GNLINSLSLFPTGFAVVLVA O29125_AR 282 LRMLPLSKRGFVMSKACLIFVISFAASLPAGSIAFIVS--QNPFYLFMAFAIPAIVSMLS Q8U2D3_PY 321 LSSLPIKRREYLLGKMLTVSLSPLTFSAILVLLSCAFNG-TEALLLIPFLASPFLTSSIG Q5JDA6_TH 328 LLSLPLERGRFLRGKLLTMAAIPSAVGV-LALLGLSLKGFSSPIYLPMAVLVPLATCGIA Q97VM1_SA 294 LLSLPAGLRSSYISKLLIILIIYL-------IDVLIFSFFNRASLSLIMLPSTITSVELS Q9HM06_TH 342 IKALPLDGNSIIRWKISAPTFIFAVISISTLAAISVKAL-MGAAFYIIIIVDMMLYFVSS Q6L2L5_PI 335 INALPINRKDIAKYKAYFSMIFYSIIITVVSIIIMAYKN-IFNLYYVFIIPDLILIFYTA O29855_AR 368 VQFSRRL-------TSEPVNVE---AVIATLISFFIVLVPAAVGGVAVLILKAPFS---S O29125_AR 340 SLIIFWQ-------KGEEIYFPEV-GFLKWIGLLLVNFGAVYAVLSPRFILSQPVA---- Q8U2D3_PY 380 ILYVKHKM------GNERIELPVL-KFYDGIVMLILSMIPFIIVAIPLFLLSVPKG---- Q5JDA6_TH 387 LHVYYH--------GTEGLALPQG-GILKSLAVWILNAVVVGIIAG-SWYLSYPIA---- Q97VM1_SA 347 LFISYNNVI-----KGKGMRLA---DPLSFIIREIEINSIIGIASILTFFANIYYS---- Q9HM06_TH 401 TVYNMNRLYRKIPDTADTVNFYSFGGQIAFITTFAFTGLIVGSADIFSLFLQDLLRLNAY Q6L2L5_PI 394 MIINLNRLIKKIPKGASTINYYSF-GVFPTIVLFIVSGIIFGLLISPGIIISEFLYHSIK O29855_AR 415 YAFPVSLAETLAVLAVFALLNRRK 439 O29125_AR 388 --DIISSVLTL----LAMTALFEK 406 Q8U2D3_PY 429 --YLVSGAIIL----VGALILSKL 447 Q5JDA6_TH 433 --LLLTAA-------IDALLLWSL 448 Q97VM1_SA 395 --LLFSVLSLI----MINIVVYKK 413 Q9HM06_TH 461 FFFLINTVIGI----IVLLFMVFR 481 Q6L2L5_PI 453 MSFIFDIIPDL----IIFLIMIKK 473 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 12TM_1 #=GF AC PF09847.11 #=GF DE Membrane protein of 12 TMs #=GF AU COGs; #=GF AU Finn RD;0000-0001-8626-2148 #=GF AU Sammut SJ;0000-0003-4472-904X #=GF SE COGs (COG3368) #=GF GA 33.20 33.20; #=GF TC 33.60 33.20; #=GF NC 33.10 32.90; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF PI DUF2074; #=GF CL CL0181 #=GF DR INTERPRO; IPR018646; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC This family carries twelve transmembrane regions. It does not have #=GF CC any characteristic nucleotide-binding-domains of the GxSGSGKST type. #=GF CC so it may not be an ATP-binding cassette transporter. However, it may #=GF CC well be a transporter of some description. ABC transporters always #=GF CC have two nucleotide binding domains; this has two unusual conserved #=GF CC sequence-motifs: 'KDhKxhhR' and 'LxxLP'. #=GF SQ 7 #=GS O29855_ARCFU/39-477 AC O29855.1 #=GS O29125_ARCFU/30-435 AC O29125.1 #=GS Q8U2D3_PYRFU/39-485 AC Q8U2D3.1 #=GS Q5JDA6_THEKO/35-482 AC Q5JDA6.1 #=GS Q97VM1_SACS2/39-451 AC Q97VM1.1 #=GS Q9HM06_THEAC/17-497 AC Q9HM06.1 #=GS Q6L2L5_PICTO/38-510 AC Q6L2L5.1 O29855_ARCFU/39-477 WIRYNALLLKIMFTFAALFSVGPAFFDDKVS....YASSLLSLFFFFLMFGTAYAHGYFQVDL...SYMHTFYSRSDISKVRFYGFFRLFDWPAVIALLS.....LLVLVGMRNPAGLLPALLGFLAVIMGALSIVILLGKRLGSVQTGR.SLRAAFFRIFGLIAWLVSIYGLYLINQLAI......YLMTFKNYEAYDSLFP.......ISYGLWISQPFSAKYAALSLFYF.ALITLLFFYAVRELSKE....EIAKHYGSLK.GWKIKRRGKMTAMVIKDFKQLFRNPQLFVIALLPIYGALM..................QLVFYIKLSEVASVLYLQIFLAITVSSFMSLERSSYITALPLTDLEMKFSKILEGLLIYF.VSMGIVAAVVIYKG.GNLINSLSLFPTGFAVVLVAVQFSRRL.......TSEPVNVE...AVIATLISFFIVLVPAAVGGVAVLILKAPFS...SYAFPVSLAETLAVLAVFALLNRRK O29125_ARCFU/30-435 SLRVQVAKSFFIMTFLGSFLCWVAFISSGLG.....LSLIFTLSLVFSQIYPAQNIAISASS....RVFEPLRYLPVRFSERMLVVF.FIDSINILAFAT...PTIAVLMVKNLYFGLYSLLWIIAAILLG.YSMVFLYYALFGVKV..RSGFSKSVL..AGILFFAVLVFAL...............RRFQEIPDLTPYLTP......................HLLLLSY..AASSATIKLSTGRVWRSILNPEIVEVKGSSR....LSSGSPLRAMLIKDFRLILRKN.ALFPLIVPLVIVMPNVVSIANMPN........LSIFIITTISTLSTIDLRIIGNLENVDF........LRMLPLSKRGFVMSKACLIFVISFAASLPAGSIAFIVS..QNPFYLFMAFAIPAIVSMLSSLIIFWQ.......KGEEIYFPEV.GFLKWIGLLLVNFGAVYAVLSPRFILSQPVA......DIISSVLTL....LAMTALFEK Q8U2D3_PYRFU/39-485 NIIWGVFLQSVMYLGLGVMVAVSILYSENEVQKAIFFSSYLIIPFILTLYSTSLATAYLLSS....KAVEPLKPLPLGNLNFIVSLTLLIENLPAFVFLI.....PASLALGNSIASLLGLLWICSTILMG.HSLALFLQIKFSGIHVGKGSVVKTLVKVAGFLI....IAGIYFIVQALMRILEDNIEVIAPIFRKYFIAFP........FAASTIYEPYKS..LVLLALYT.LPFLALYFYDLKRLGEVL...EGIKTYGKVATKYKLTVANPVTAMFRKDYRIIFRKNPYLGTFLSPLLMSIYFIYNLAKEGFPVM.....MTLFSIMGISVLGLVMLDPAFAMDREVF......PFLSSLPIKRREYLLGKMLTVSLSPLTFSAILVLLSCAFNG.TEALLLIPFLASPFLTSSIGILYVKHKM......GNERIELPVL.KFYDGIVMLILSMIPFIIVAIPLFLLSVPKG......YLVSGAIIL....VGALILSKL Q5JDA6_THEKO/35-482 DLKKTLLFQTAMYAVFGLML.FPSLKGERDA.VLVMASTYAILPFIIAFYATVTNSSYIASL....DLFKPLLPLPIKLGGRYMSVLLLLESLPVMAFMV..PGAVRIGMVVSATSGLLVLLWSAVGLMLG.HVFGLLVYYSFGKTSSGRFADLKSLAKALGVIL....IFGLFYGFSYFQDYVLQNYTSIKESLGGYEFIYP........LSVLSVDRPSFS..APLAGIYI.AILGVAYYVLISRLWVRI..SEGSYTSGRRRRAGGLGVYPPELALMVKDFKTALRNTPVLTGLLVPIVIPIINVAGIFSNPDIGAFGGRLATITFVAALGWVSAVSVETLTKIEVKSF......ELLLSLPLERGRFLRGKLLTMAAIPSAVGV.LALLGLSLKGFSSPIYLPMAVLVPLATCGIALHVYYH........GTEGLALPQG.GILKSLAVWILNAVVVGIIAG.SWYLSYPIA......LLLTAA.......IDALLLWSL Q97VM1_SACS2/39-451 NAVTIKISNIIAYTIATIVSASISLINKDAP....FSFIFLDLIILANIFTTGLNVIFFVTNY...DLKTFLLSLPLSERDVNRAVFRGIFEFFYYGFLA..SIVIAPISTYMITSSVLQALMAELEIIFF.FSLSFALVMLLGKRI..RLGITSALFRIGTSLIWIVFIMLPYGL...........TFKYVTIPTYILPIFP........FGFLNIEG......LLISLLYTGLSVFFAYKQSLKFLSFRL........NSQYSTKYSIKLRSPLITYLYKDIRGLLRVPQASFLLTIPVFALIFSFFAPV............YAIFYTIFMITTSSIMLIL...LEASGM......QLLLSLPAGLRSSYISKLLIILIIYL.......IDVLIFSFFNRASLSLIMLPSTITSVELSLFISYNNVI.....KGKGMRLA...DPLSFIIREIEINSIIGIASILTFFANIYYS......LLFSVLSLI....MINIVVYKK Q9HM06_THEAC/17-497 YVNISYGATSFSFIVFSLILVAPSLMEHRIY....TLSSVVLLLFVYSLFINISNSLLFFVSVNINHILDPLRILPVDFPDHVIAVSWFIYTGSSSLFAVLPAIFLAAFLLGDPYILVIGLIWSIFSVLLG.YIIGSSIFVAFGSRISGKRTRSTNILRNVGRIVFLVFVFAIFEIILYNANIV...NGIIPRLPYPYSYFIPIFNIQSTVFFFHGIYMQATG..FIISMVYT.ALASFAFIYVNRKAFYRLLEP.TARNQSRVKTQMKAEVRSRPFSFFSKDLKISSRKSQNLVLLIMPLFFVFPTIMSEVLYAPTSKADPIILYNAMVAFVIVTSSFYSILFLVIEGNGI......SFIKALPLDGNSIIRWKISAPTFIFAVISISTLAAISVKAL.MGAAFYIIIIVDMMLYFVSSTVYNMNRLYRKIPDTADTVNFYSFGGQIAFITTFAFTGLIVGSADIFSLFLQDLLRLNAYFFFLINTVIGI....IVLLFMVFR Q6L2L5_PICTO/38-510 TILLYYISNSLSFLFFSIVLNGIYYVKGNTN....DISSFGIILFMYIFVIGIYSSLTYINGISINNLLSPVRSLPIKVNTDVPFLSWFIYTGSSYIFIIIPSLLFYYFLVHNLNTIILGLIYAFAMLLFG.FIITAIAFI.....YSSRKPRAHTSLNNFLRILLIFVFLGFFYLIIYDPNILRAYSIYISSLPVYIKYIAFPLNIDYAVYFHPDIIATFFE..YLSSFIIL.LIFFFIYKKIRSRLFYSL..EYSEEVKSTEVTRTKIKRDSISVSFIKKDIKITARKSQNLTYILMPIIFVLPFLFTIISSRQPFLS....LMFSILSLSILISSFYPIFTLIIENNGI......LIINALPINRKDIAKYKAYFSMIFYSIIITVVSIIIMAYKN.IFNLYYVFIIPDLILIFYTAMIINLNRLIKKIPKGASTINYYSF.GVFPTIVLFIVSGIIFGLLISPGIIISEFLYHSIKMSFIFDIIPDL....IIFLIMIKK #=GC seq_cons slhhthhhpphhahhhulhlsssuhhscphs....hhSohhhL.Flhshahsshsshhhhss....clhcPLhsLPlp.tschhulhhhI.shsshsFhs....hltshhlhs.hsulLsLLauhhsllhG.aslshhlhhhhGthhsuRhuhspslh+.hGhllhhh.lhulahl..h.........hhh.pl.thh.hlhP........hhh.sI.t...t..hlluhlYh.hhhhhhahhshp+Lhhpl....h.cspuphppthplphtu..huhhhKDh+hhhRps.sLshllhPlhhsl..lhs.h............hhlhhlthh.shSslhl.hhhhlEssuh.......hlpuLPlscpphhhuKhhhhhlI.hhhuh.hshhshhhph.tpshhhlhhlssshhsshluhhhshpp.......su-slph..h.uhlshIshhllshlhhulssh.shhLs..hu......hlloss.hl....lhhLlhhc+ // """, ) def check_alignment_pfam4(self, alignment): """Check the alignment obtained by parsing Pfam record 3Beta_HSD.""" self.assertEqual(alignment.annotations["identifier"], "3Beta_HSD") self.assertEqual(alignment.annotations["accession"], "PF01073.21") self.assertEqual( alignment.annotations["definition"], "3-beta hydroxysteroid dehydrogenase/isomerase family", ) self.assertEqual(len(alignment.annotations["author"]), 2) self.assertEqual( alignment.annotations["author"][0], "Finn RD;0000-0001-8626-2148" ) self.assertEqual( alignment.annotations["author"][1], "Bateman A;0000-0002-6982-4660" ) self.assertEqual( alignment.annotations["source of seed"], "Pfam-B_504 (release 3.0)" ) self.assertEqual(alignment.annotations["gathering method"], "22.00 22.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "22.00 22.00;") self.assertEqual(alignment.annotations["noise cutoff"], "21.90 21.90;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual(len(alignment.annotations["wikipedia"]), 1) self.assertEqual( alignment.annotations["wikipedia"][0], "3β-Hydroxysteroid_dehydrogenase" ) self.assertEqual(alignment.annotations["clan"], "CL0063") self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "1562516") self.assertEqual( alignment.annotations["references"][0]["title"], "Structure and tissue-specific expression of 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase genes in human and rat classical and peripheral steroidogenic tissues.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Labrie F, Simard J, Luu-The V, Pelletier G, Belanger A, Lachance Y, Zhao HF, Labrie C, Breton N, de Launoit Y, et al", ) self.assertEqual( alignment.annotations["references"][0]["location"], "J Steroid Biochem Mol Biol 1992;41:421-435.", ) self.assertEqual(len(alignment.annotations["database references"]), 3) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR002225;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "HOMSTRAD; Epimerase;", ) self.assertEqual( alignment.annotations["database references"][2]["reference"], "SO; 0100021; polypeptide_conserved_region;", ) self.assertEqual( alignment.annotations["comment"], "The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones.", ) self.assertEqual(len(alignment.sequences), 8) self.assertEqual(alignment.sequences[0].id, "3BHS_FOWPN/7-287") self.assertEqual(alignment.sequences[1].id, "Q98318_MCV1/5-278") self.assertEqual(alignment.sequences[2].id, "3BHS_VACCW/5-274") self.assertEqual(alignment.sequences[3].id, "3BHS1_HUMAN/7-288") self.assertEqual(alignment.sequences[4].id, "3BHS1_MOUSE/7-288") self.assertEqual(alignment.sequences[5].id, "O22813_ARATH/15-299") self.assertEqual(alignment.sequences[6].id, "HSDD3_ARATH/16-287") self.assertEqual(alignment.sequences[7].id, "ERG26_YEAST/8-280") self.assertEqual(alignment.sequences[0].annotations["accession"], "Q67477.2") self.assertEqual(alignment.sequences[1].annotations["accession"], "Q98318.1") self.assertEqual(alignment.sequences[2].annotations["accession"], "P26670.1") self.assertEqual(alignment.sequences[3].annotations["accession"], "P14060.2") self.assertEqual(alignment.sequences[4].annotations["accession"], "P24815.3") self.assertEqual(alignment.sequences[5].annotations["accession"], "O22813.1") self.assertEqual(alignment.sequences[6].annotations["accession"], "A9X4U2.2") self.assertEqual(alignment.sequences[7].annotations["accession"], "P53199.1") self.assertEqual( alignment.sequences[0].seq, "VVTGGCGFLGRHIINNLILFESSLKEVRVYDIRIDQWLLDLVEKCNIIKIVPVIGDVRNKSTLDEALRSADVVIHIASINDVAGKFTNDSIMDVNINGTKNVVDSCLYNGVRVLVYTSSYSAVGPNFLGDAMIRGNENTYYQSNHKEAYPLSKQLSEKYILEANGTMSNIGLRLCTCALRPLGVFGEYCPVLETLYRRSYKSRKMYKYADDKVFHSRVYAGNVAWMHILAARNMIENGQHSPLCNNVYYCYDTSPTEHYHDFNMHFFNQLGMDLRNTCLPL", ) self.assertEqual( alignment.sequences[1].seq, "AVTGGGGFIGSYIVRALLQCERTLIELRVIDVRWGTKVSSRNVNVVYIYCDVCDTARLCAALEGVDVLIHTAGLVDVMGEYSEDEIYRANVHGTHSALSACVCAGVRFVVYTSSMEVVGPNMRAEPFVGDEKTEYESCHQHCYPRSKAEAEELVLSSNGRRVRGGQRMLTCALRPPGVYGEGNQLLLRLAKNYVRMGLHVPRTVCENALQSRVYVGNVAWMHVLAARALQEPDSRLPGNAYFCYDHSPCMDYEAFNVMLLRSFGVELGGPRLPR", ) self.assertEqual( alignment.sequences[2].seq, "AVTGGAGFLGRYIVKLLISADDVQEIRVIDIVEDPQPITSKVKVINYIQCDINDFDKVREALDGVNLIIHTAALVDVFGKYTDNEIMKVNYYGTQTILAACVDLGIKYLIYTSSMEAIGPNKHGDPFIGHEHTLYDISPGHVYAKSKRMAEQLVMKANNSVIMNGAKLYTCCLRPTGIYGEGDKLTKVFYEQCKQHGNIMYRTVDDDAVHSRVYVGNVAWMHVLAAKYIQYPGSEIKGNAYFCYDYSPSCSYDMFNLLLMKPLGIEQGSR", ) self.assertEqual( alignment.sequences[3].seq, "LVTGAGGFLGQRIIRLLVKEKELKEIRVLDKAFGPELREEFSKLQNKTKLTVLEGDILDEPFLKRACQDVSVIIHTACIIDVFGVTHRESIMNVNVKGTQLLLEACVQASVPVFIYTSSIEVAGPNSYKEIIQNGHEEEPLENTWPAPYPHSKKLAEKAVLAANGWNLKNGGTLYTCALRPMYIYGEGSRFLSASINEALNNNGILSSVGKFSTVNPVYVGNVAWAHILALRALQDPKKAPSIRGQFYYISDDTPHQSYDNLNYTLSKEFGLRLDSRWSFPL", ) self.assertEqual( alignment.sequences[4].seq, "LVTGAGGFVGQRIIKMLVQEKELQEVRALDKVFRPETKEEFSKLQTKTKVTVLEGDILDAQCLRRACQGISVVIHTAAVIDVTGVIPRQTILDVNLKGTQNLLEACVQASVPAFIFCSSVDVAGPNSYKKIVLNGHEEQNHESTWSDPYPYSKKMAEKAVLAANGSMLKNGGTLNTCALRPMYIYGERSPFIFNAIIRALKNKGILCVTGKFSIANPVYVENVAWAHILAARGLRDPKKSTSIQGQFYYISDDTPHQSYDDLNYTLSKEWGLRPNASWSLPL", ) self.assertEqual( alignment.sequences[5].seq, "VVTGGLGFVGAALCLELVRRGARQVRSFDLRHSSPWSDDLKNSGVRCIQGDVTKKQDVDNALDGADCVLHLASYGMSGKEMLRFGRCDEVNINGTCNVLEAAFKHEITRIVYVSTYNVVFGGKEILNGNEGLPYFPLDDHVDAYSRTKSIAEQLVLKSNGRPFKNGGKRMYTCAIRPAAIYGPGEDRHLPRIVTLTKLGLALFKIGEPSVKSDWIYVENLVLAIILASMGLLDDIPGREGQPVAAGQPYFVSDGYPVNTFEFLRPLLKSLDYDLPKCTISVPFAL", ) self.assertEqual( alignment.sequences[6].seq, "VVLGGRGFIGRSLVSRLLRLGNWTVRVADSGHTLHLDESDSLLEDALSSGRASYHCVDVRDKPQIVKVTEGSYVVFYMGATDLRSHDYFDCYKVIVQGTRNVISACRESGVRKLIYNSTADVVFDGSQPIRDGDESLRRPLKFQSMLTDFKAQAEALIKLANNRDGLLTCALRSSIVFGPGDTEFVPFLVNLAKSGYAKFILGSGENISDFTYSENVSHAHICAVKALDSQMEFVAGKEFFITNLKPVRFWDFVSHIVEGLGYPRPSIKLPV", ) self.assertEqual( alignment.sequences[7].seq, "LIIGGSGFLGLHLIQQFFDINPKPDIHIFDVRDLPEKLSKQFTFNVDDIKFHKGDLTSPDDMENAINESKANVVVHCASPMHGQNPDIYDIVNVKGTRNVIDMCKKCGVNILVYTSSAGVIFNGQDVHNADETWPIPEVPMDAYNETKAIAEDMVLKANDPSSDFYTVALRPAGIFGPGDRQLVPGLRQVAKLGQSKFQIGDNNNLFDWTYAGNVADAHVLAAQKLLDPKTRTAVSGETFFITNDTPTYFWALARTVWKADGHIDKHVIVLKR", ) self.assertEqual( alignment[0], "VVTGGCGFLGRHIINNLILFESSLKEVRVYD------IRIDQWLLDLVEKCNII-KIVPVIGDVRNKSTLDEALRSADVVIHIASINDVAG-KFTNDSIMDVNINGTKNVVDSCLYNGVRVLVYTSSYSAVGPNFLGDAMIRGNENTYYQSN--HKEAYPLSKQLSEKYILEANG-TMSNIGLRLCTCALRPLGVFGEYCPVLETLYRRSYKSR-KMYKYADDKVFHSRVYAGNVAWMHILAARNMIENGQ----HSPLCNNVYYCYDTSPTEHYHDFNMHFFNQLGMDLRN-T---CLPL", ) self.assertEqual( alignment[1], "AVTGGGGFIGSYIVRALLQCERTLIELRVID------VRWGTKV--SSRNVNVV----YIYCDVCDTARLCAALEGVDVLIHTAGLVDVMG-EYSEDEIYRANVHGTHSALSACVCAGVRFVVYTSSMEVVGPNMRAEPFV-GDEKTEYESC--HQHCYPRSKAEAEELVLSSNGRRVRGGQ-RMLTCALRPPGVYGEGNQLLLRLAKNYVRMGLHVPRTVCENALQSRVYVGNVAWMHVLAARALQEP------DSRLPGNAYFCYDHSPCMDYEAFNVMLLRSFGVELGGP----RLPR", ) self.assertEqual( alignment[2], "AVTGGAGFLGRYIVKLLISADD-VQEIRVID------IVEDPQP--ITSKVKVIN---YIQCDINDFDKVREALDGVNLIIHTAALVDVFG-KYTDNEIMKVNYYGTQTILAACVDLGIKYLIYTSSMEAIGPNKHGDPFI-GHEHTLYDIS--PGHVYAKSKRMAEQLVMKANNSVIMNGA-KLYTCCLRPTGIYGEGDKLTKVFYEQCKQHGNIMYRTVDDDAVHSRVYVGNVAWMHVLAAKYIQYP------GSEIKGNAYFCYDYSPSCSYDMFNLLLMKPLGIEQGSR--------", ) self.assertEqual( alignment[3], "LVTGAGGFLGQRIIRLLVKEKE-LKEIRVLD------KAFGPELREEFSKLQNKTKLTVLEGDILDEPFLKRACQDVSVIIHTACIIDVFG-VTHRESIMNVNVKGTQLLLEACVQASVPVFIYTSSIEVAGPNSYKEIIQNGHEEEPLENT--WPAPYPHSKKLAEKAVLAANGWNLKNGG-TLYTCALRPMYIYGEGSRFLSASINEALNNN-GILSSVGKFSTVNPVYVGNVAWAHILALRALQDPKK----APSIRGQFYYISDDTPHQSYDNLNYTLSKEFGLRLDSRW---SFPL", ) self.assertEqual( alignment[4], "LVTGAGGFVGQRIIKMLVQEKE-LQEVRALD------KVFRPETKEEFSKLQTKTKVTVLEGDILDAQCLRRACQGISVVIHTAAVIDVTG-VIPRQTILDVNLKGTQNLLEACVQASVPAFIFCSSVDVAGPNSYKKIVLNGHEEQNHEST--WSDPYPYSKKMAEKAVLAANGSMLKNGG-TLNTCALRPMYIYGERSPFIFNAIIRALKNKGILCVTGKFSI-ANPVYVENVAWAHILAARGLRDPKK----STSIQGQFYYISDDTPHQSYDDLNYTLSKEWGLRPNASW---SLPL", ) self.assertEqual( alignment[5], "VVTGGLGFVGAALCLELVRRG--ARQVRSFD------LRHSSPWSDDLKNSGVR----CIQGDVTKKQDVDNALDGADCVLHLASYGMSGKEMLRFGRCDEVNINGTCNVLEAAFKHEITRIVYVSTYNVVFG---GKEILNGNEGLPYFPLDDHVDAYSRTKSIAEQLVLKSNGRPFKNGGKRMYTCAIRPAAIYGPGEDRHLPRIVTLTKLGLALFKIGEPSVKSDWIYVENLVLAIILASMGLLDDIPGREGQPVAAGQPYFVSDGYPVN-TFEFLRPLLKSLDYDLPKCTISVPFAL", ) self.assertEqual( alignment[6], "VVLGGRGFIGRSLVSRLLRLGN--WTVRVADSGHTLHLDESDSLLEDALSSGRAS---YHCVDVRDKPQIVKVTEGSYVVFYM-GATDLRS-HDYFD-CYKVIVQGTRNVISACRESGVRKLIYNSTADVVFD--GSQPIRDGDESLRRPLK--FQSMLTDFKAQAEALIKLANN---RDG---LLTCALRSSIVFGPGDTEFVPFLVNLAKSGYAKFILGSGENISDFTYSENVSHAHICAVKALDSQ------MEFVAGKEFFITNLKPVR-FWDFVSHIVEGLGYPRPS-I---KLPV", ) self.assertEqual( alignment[7], "LIIGGSGFLGLHLIQQFFDINP-KPDIHIFD------VRDLPEKLSKQFTFNVDDI-KFHKGDLTSPDDMENAINESKANVVVHCASPMHG--QNPDIYDIVNVKGTRNVIDMCKKCGVNILVYTSSAGVIFN---GQDVHNADETWPIPEV--PMDAYNETKAIAEDMVLKAND-----PSSDFYTVALRPAGIFGPGDRQLVPGLRQVAKLGQSKFQIGDNNNLFDWTYAGNVADAHVLAAQKLLDPKT----RTAVSGETFFITNDTPTY-FWALARTVWKADGHIDKHVI---VLKR", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "lVTGGuGFlGppIlptLlptcp.lpElRVhD......lchssphh-chppsslts...hlpGDlpDpsplccAlcGssVlIHsAulsDVtG.hhsp-pIhcVNlpGTpNlL-AClpsGVphllYTSSh-VlGPN.hucsllsGcEpp.apss..atcsYscSKphAEchVLpANG..h+NGu.cLhTCALRPsuIYGEGsphlhshlppshKpG.thaphucssshpshVYVGNVAWAHILAA+uLp-Ph.....poslsGpsYFloDsoPsppYcsFNhpLhKshGhchsu.h...sLPl", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 0, 21, 22, 23, 24, 31, 31, 38, 40, 48, 48, 49, 50, 51, 76, 77, 84, 84, 85, 89, 90, 125, 127, 128, 133, 134, 144, 144, 165, 165, 167, 169, 170, 171, 172, 173, 203, 203, 213, 214, 237, 239, 239, 257, 258, 276, 276, 277, 277, 281], [ 0, 21, 22, 23, 24, 31, 31, 38, 38, 46, 46, 46, 46, 46, 71, 72, 79, 79, 80, 84, 85, 120, 122, 123, 128, 128, 138, 138, 159, 160, 162, 164, 165, 166, 166, 167, 197, 198, 208, 209, 232, 232, 232, 250, 251, 269, 270, 270, 270, 274], [ 0, 21, 22, 22, 23, 30, 30, 37, 37, 45, 46, 46, 46, 46, 71, 72, 79, 79, 80, 84, 85, 120, 122, 123, 128, 128, 138, 138, 159, 160, 162, 164, 165, 166, 166, 167, 197, 198, 208, 209, 232, 232, 232, 250, 251, 269, 270, 270, 270, 270], [ 0, 21, 22, 22, 23, 30, 30, 37, 39, 47, 48, 49, 50, 51, 76, 77, 84, 84, 85, 89, 90, 125, 127, 128, 133, 134, 144, 144, 165, 166, 168, 170, 171, 172, 172, 173, 203, 203, 213, 214, 237, 239, 239, 257, 258, 276, 277, 278, 278, 282], [ 0, 21, 22, 22, 23, 30, 30, 37, 39, 47, 48, 49, 50, 51, 76, 77, 84, 84, 85, 89, 90, 125, 127, 128, 133, 134, 144, 144, 165, 166, 168, 170, 171, 172, 172, 173, 203, 204, 214, 214, 237, 239, 239, 257, 258, 276, 277, 278, 278, 282], [ 0, 21, 21, 21, 22, 29, 29, 36, 38, 46, 46, 46, 46, 46, 71, 72, 79, 80, 81, 85, 86, 121, 121, 121, 126, 127, 137, 139, 160, 161, 163, 165, 166, 167, 168, 169, 199, 200, 210, 211, 234, 236, 240, 258, 258, 276, 277, 278, 281, 285], [ 0, 21, 22, 22, 22, 29, 35, 42, 44, 52, 53, 53, 53, 53, 78, 78, 85, 85, 86, 90, 90, 125, 125, 126, 131, 132, 142, 142, 163, 163, 163, 165, 166, 166, 166, 166, 196, 197, 207, 208, 231, 231, 231, 249, 249, 267, 267, 268, 268, 272], [ 0, 21, 22, 22, 23, 30, 30, 37, 39, 47, 48, 49, 49, 50, 75, 76, 83, 83, 83, 87, 88, 123, 123, 123, 128, 129, 139, 139, 160, 160, 160, 160, 161, 162, 163, 164, 194, 195, 205, 206, 229, 231, 231, 249, 249, 267, 268, 269, 269, 273] ] # fmt: on ), ) ) self.assertEqual( str(alignment), """\ 3BHS_FOWP 0 VVTGGCGFLGRHIINNLILFESSLKEVRVYD------IRIDQWLLDLVEKCNII-KIVPV Q98318_MC 0 AVTGGGGFIGSYIVRALLQCERTLIELRVID------VRWGTKV--SSRNVNVV----YI 3BHS_VACC 0 AVTGGAGFLGRYIVKLLISADD-VQEIRVID------IVEDPQP--ITSKVKVIN---YI 3BHS1_HUM 0 LVTGAGGFLGQRIIRLLVKEKE-LKEIRVLD------KAFGPELREEFSKLQNKTKLTVL 3BHS1_MOU 0 LVTGAGGFVGQRIIKMLVQEKE-LQEVRALD------KVFRPETKEEFSKLQTKTKVTVL O22813_AR 0 VVTGGLGFVGAALCLELVRRG--ARQVRSFD------LRHSSPWSDDLKNSGVR----CI HSDD3_ARA 0 VVLGGRGFIGRSLVSRLLRLGN--WTVRVADSGHTLHLDESDSLLEDALSSGRAS---YH ERG26_YEA 0 LIIGGSGFLGLHLIQQFFDINP-KPDIHIFD------VRDLPEKLSKQFTFNVDDI-KFH 3BHS_FOWP 53 IGDVRNKSTLDEALRSADVVIHIASINDVAG-KFTNDSIMDVNINGTKNVVDSCLYNGVR Q98318_MC 48 YCDVCDTARLCAALEGVDVLIHTAGLVDVMG-EYSEDEIYRANVHGTHSALSACVCAGVR 3BHS_VACC 48 QCDINDFDKVREALDGVNLIIHTAALVDVFG-KYTDNEIMKVNYYGTQTILAACVDLGIK 3BHS1_HUM 53 EGDILDEPFLKRACQDVSVIIHTACIIDVFG-VTHRESIMNVNVKGTQLLLEACVQASVP 3BHS1_MOU 53 EGDILDAQCLRRACQGISVVIHTAAVIDVTG-VIPRQTILDVNLKGTQNLLEACVQASVP O22813_AR 48 QGDVTKKQDVDNALDGADCVLHLASYGMSGKEMLRFGRCDEVNINGTCNVLEAAFKHEIT HSDD3_ARA 55 CVDVRDKPQIVKVTEGSYVVFYM-GATDLRS-HDYFD-CYKVIVQGTRNVISACRESGVR ERG26_YEA 52 KGDLTSPDDMENAINESKANVVVHCASPMHG--QNPDIYDIVNVKGTRNVIDMCKKCGVN 3BHS_FOWP 112 VLVYTSSYSAVGPNFLGDAMIRGNENTYYQSN--HKEAYPLSKQLSEKYILEANG-TMSN Q98318_MC 107 FVVYTSSMEVVGPNMRAEPFV-GDEKTEYESC--HQHCYPRSKAEAEELVLSSNGRRVRG 3BHS_VACC 107 YLIYTSSMEAIGPNKHGDPFI-GHEHTLYDIS--PGHVYAKSKRMAEQLVMKANNSVIMN 3BHS1_HUM 112 VFIYTSSIEVAGPNSYKEIIQNGHEEEPLENT--WPAPYPHSKKLAEKAVLAANGWNLKN 3BHS1_MOU 112 AFIFCSSVDVAGPNSYKKIVLNGHEEQNHEST--WSDPYPYSKKMAEKAVLAANGSMLKN O22813_AR 108 RIVYVSTYNVVFG---GKEILNGNEGLPYFPLDDHVDAYSRTKSIAEQLVLKSNGRPFKN HSDD3_ARA 112 KLIYNSTADVVFD--GSQPIRDGDESLRRPLK--FQSMLTDFKAQAEALIKLANN---RD ERG26_YEA 110 ILVYTSSAGVIFN---GQDVHNADETWPIPEV--PMDAYNETKAIAEDMVLKAND----- 3BHS_FOWP 169 IGLRLCTCALRPLGVFGEYCPVLETLYRRSYKSR-KMYKYADDKVFHSRVYAGNVAWMHI Q98318_MC 164 GQ-RMLTCALRPPGVYGEGNQLLLRLAKNYVRMGLHVPRTVCENALQSRVYVGNVAWMHV 3BHS_VACC 164 GA-KLYTCCLRPTGIYGEGDKLTKVFYEQCKQHGNIMYRTVDDDAVHSRVYVGNVAWMHV 3BHS1_HUM 170 GG-TLYTCALRPMYIYGEGSRFLSASINEALNNN-GILSSVGKFSTVNPVYVGNVAWAHI 3BHS1_MOU 170 GG-TLNTCALRPMYIYGERSPFIFNAIIRALKNKGILCVTGKFSI-ANPVYVENVAWAHI O22813_AR 165 GGKRMYTCAIRPAAIYGPGEDRHLPRIVTLTKLGLALFKIGEPSVKSDWIYVENLVLAII HSDD3_ARA 165 G---LLTCALRSSIVFGPGDTEFVPFLVNLAKSGYAKFILGSGENISDFTYSENVSHAHI ERG26_YEA 160 PSSDFYTVALRPAGIFGPGDRQLVPGLRQVAKLGQSKFQIGDNNNLFDWTYAGNVADAHV 3BHS_FOWP 228 LAARNMIENGQ----HSPLCNNVYYCYDTSPTEHYHDFNMHFFNQLGMDLRN-T---CLP Q98318_MC 223 LAARALQEP------DSRLPGNAYFCYDHSPCMDYEAFNVMLLRSFGVELGGP----RLP 3BHS_VACC 223 LAAKYIQYP------GSEIKGNAYFCYDYSPSCSYDMFNLLLMKPLGIEQGSR------- 3BHS1_HUM 228 LALRALQDPKK----APSIRGQFYYISDDTPHQSYDNLNYTLSKEFGLRLDSRW---SFP 3BHS1_MOU 228 LAARGLRDPKK----STSIQGQFYYISDDTPHQSYDDLNYTLSKEWGLRPNASW---SLP O22813_AR 225 LASMGLLDDIPGREGQPVAAGQPYFVSDGYPVN-TFEFLRPLLKSLDYDLPKCTISVPFA HSDD3_ARA 222 CAVKALDSQ------MEFVAGKEFFITNLKPVR-FWDFVSHIVEGLGYPRPS-I---KLP ERG26_YEA 220 LAAQKLLDPKT----RTAVSGETFFITNDTPTY-FWALARTVWKADGHIDKHVI---VLK 3BHS_FOWP 280 L 281 Q98318_MC 273 R 274 3BHS_VACC 270 - 270 3BHS1_HUM 281 L 282 3BHS1_MOU 281 L 282 O22813_AR 284 L 285 HSDD3_ARA 271 V 272 ERG26_YEA 272 R 273 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 3Beta_HSD #=GF AC PF01073.21 #=GF DE 3-beta hydroxysteroid dehydrogenase/isomerase family #=GF AU Finn RD;0000-0001-8626-2148 #=GF AU Bateman A;0000-0002-6982-4660 #=GF SE Pfam-B_504 (release 3.0) #=GF GA 22.00 22.00; #=GF TC 22.00 22.00; #=GF NC 21.90 21.90; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF CL CL0063 #=GF WK 3β-Hydroxysteroid_dehydrogenase #=GF RN [1] #=GF RM 1562516 #=GF RT Structure and tissue-specific expression of 3 beta-hydroxysteroid #=GF RT dehydrogenase/5-ene-4-ene isomerase genes in human and rat classical #=GF RT and peripheral steroidogenic tissues. #=GF RA Labrie F, Simard J, Luu-The V, Pelletier G, Belanger A, Lachance Y, Zhao HF, Labrie C, Breton N, de Launoit Y, et al #=GF RL J Steroid Biochem Mol Biol 1992;41:421-435. #=GF DR INTERPRO; IPR002225; #=GF DR HOMSTRAD; Epimerase; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase #=GF CC (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 #=GF CC beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors #=GF CC into the corresponding 4-ene-ketosteroids necessary for the formation #=GF CC of all classes of steroid hormones. #=GF SQ 8 #=GS 3BHS_FOWPN/7-287 AC Q67477.2 #=GS Q98318_MCV1/5-278 AC Q98318.1 #=GS 3BHS_VACCW/5-274 AC P26670.1 #=GS 3BHS1_HUMAN/7-288 AC P14060.2 #=GS 3BHS1_MOUSE/7-288 AC P24815.3 #=GS O22813_ARATH/15-299 AC O22813.1 #=GS HSDD3_ARATH/16-287 AC A9X4U2.2 #=GS ERG26_YEAST/8-280 AC P53199.1 3BHS_FOWPN/7-287 VVTGGCGFLGRHIINNLILFESSLKEVRVYD......IRIDQWLLDLVEKCNII.KIVPVIGDVRNKSTLDEALRSADVVIHIASINDVAG.KFTNDSIMDVNINGTKNVVDSCLYNGVRVLVYTSSYSAVGPNFLGDAMIRGNENTYYQSN..HKEAYPLSKQLSEKYILEANG.TMSNIGLRLCTCALRPLGVFGEYCPVLETLYRRSYKSR.KMYKYADDKVFHSRVYAGNVAWMHILAARNMIENGQ....HSPLCNNVYYCYDTSPTEHYHDFNMHFFNQLGMDLRN.T...CLPL Q98318_MCV1/5-278 AVTGGGGFIGSYIVRALLQCERTLIELRVID......VRWGTKV..SSRNVNVV....YIYCDVCDTARLCAALEGVDVLIHTAGLVDVMG.EYSEDEIYRANVHGTHSALSACVCAGVRFVVYTSSMEVVGPNMRAEPFV.GDEKTEYESC..HQHCYPRSKAEAEELVLSSNGRRVRGGQ.RMLTCALRPPGVYGEGNQLLLRLAKNYVRMGLHVPRTVCENALQSRVYVGNVAWMHVLAARALQEP......DSRLPGNAYFCYDHSPCMDYEAFNVMLLRSFGVELGGP....RLPR 3BHS_VACCW/5-274 AVTGGAGFLGRYIVKLLISADD.VQEIRVID......IVEDPQP..ITSKVKVIN...YIQCDINDFDKVREALDGVNLIIHTAALVDVFG.KYTDNEIMKVNYYGTQTILAACVDLGIKYLIYTSSMEAIGPNKHGDPFI.GHEHTLYDIS..PGHVYAKSKRMAEQLVMKANNSVIMNGA.KLYTCCLRPTGIYGEGDKLTKVFYEQCKQHGNIMYRTVDDDAVHSRVYVGNVAWMHVLAAKYIQYP......GSEIKGNAYFCYDYSPSCSYDMFNLLLMKPLGIEQGSR........ 3BHS1_HUMAN/7-288 LVTGAGGFLGQRIIRLLVKEKE.LKEIRVLD......KAFGPELREEFSKLQNKTKLTVLEGDILDEPFLKRACQDVSVIIHTACIIDVFG.VTHRESIMNVNVKGTQLLLEACVQASVPVFIYTSSIEVAGPNSYKEIIQNGHEEEPLENT..WPAPYPHSKKLAEKAVLAANGWNLKNGG.TLYTCALRPMYIYGEGSRFLSASINEALNNN.GILSSVGKFSTVNPVYVGNVAWAHILALRALQDPKK....APSIRGQFYYISDDTPHQSYDNLNYTLSKEFGLRLDSRW...SFPL 3BHS1_MOUSE/7-288 LVTGAGGFVGQRIIKMLVQEKE.LQEVRALD......KVFRPETKEEFSKLQTKTKVTVLEGDILDAQCLRRACQGISVVIHTAAVIDVTG.VIPRQTILDVNLKGTQNLLEACVQASVPAFIFCSSVDVAGPNSYKKIVLNGHEEQNHEST..WSDPYPYSKKMAEKAVLAANGSMLKNGG.TLNTCALRPMYIYGERSPFIFNAIIRALKNKGILCVTGKFSI.ANPVYVENVAWAHILAARGLRDPKK....STSIQGQFYYISDDTPHQSYDDLNYTLSKEWGLRPNASW...SLPL O22813_ARATH/15-299 VVTGGLGFVGAALCLELVRRG..ARQVRSFD......LRHSSPWSDDLKNSGVR....CIQGDVTKKQDVDNALDGADCVLHLASYGMSGKEMLRFGRCDEVNINGTCNVLEAAFKHEITRIVYVSTYNVVFG...GKEILNGNEGLPYFPLDDHVDAYSRTKSIAEQLVLKSNGRPFKNGGKRMYTCAIRPAAIYGPGEDRHLPRIVTLTKLGLALFKIGEPSVKSDWIYVENLVLAIILASMGLLDDIPGREGQPVAAGQPYFVSDGYPVN.TFEFLRPLLKSLDYDLPKCTISVPFAL HSDD3_ARATH/16-287 VVLGGRGFIGRSLVSRLLRLGN..WTVRVADSGHTLHLDESDSLLEDALSSGRAS...YHCVDVRDKPQIVKVTEGSYVVFYM.GATDLRS.HDYFD.CYKVIVQGTRNVISACRESGVRKLIYNSTADVVFD..GSQPIRDGDESLRRPLK..FQSMLTDFKAQAEALIKLANN...RDG...LLTCALRSSIVFGPGDTEFVPFLVNLAKSGYAKFILGSGENISDFTYSENVSHAHICAVKALDSQ......MEFVAGKEFFITNLKPVR.FWDFVSHIVEGLGYPRPS.I...KLPV ERG26_YEAST/8-280 LIIGGSGFLGLHLIQQFFDINP.KPDIHIFD......VRDLPEKLSKQFTFNVDDI.KFHKGDLTSPDDMENAINESKANVVVHCASPMHG..QNPDIYDIVNVKGTRNVIDMCKKCGVNILVYTSSAGVIFN...GQDVHNADETWPIPEV..PMDAYNETKAIAEDMVLKAND.....PSSDFYTVALRPAGIFGPGDRQLVPGLRQVAKLGQSKFQIGDNNNLFDWTYAGNVADAHVLAAQKLLDPKT....RTAVSGETFFITNDTPTY.FWALARTVWKADGHIDKHVI...VLKR #=GC seq_cons lVTGGuGFlGppIlptLlptcp.lpElRVhD......lchssphh-chppsslts...hlpGDlpDpsplccAlcGssVlIHsAulsDVtG.hhsp-pIhcVNlpGTpNlL-AClpsGVphllYTSSh-VlGPN.hucsllsGcEpp.apss..atcsYscSKphAEchVLpANG..h+NGu.cLhTCALRPsuIYGEGsphlhshlppshKpG.thaphucssshpshVYVGNVAWAHILAA+uLp-Ph.....poslsGpsYFloDsoPsppYcsFNhpLhKshGhchsu.h...sLPl // """, ) def check_alignment_pfam5(self, alignment): """Check the alignment obtained by parsing Pfam record ArsP_1.""" self.assertEqual(alignment.annotations["identifier"], "ArsP_1") self.assertEqual(alignment.annotations["accession"], "PF03773.15") self.assertEqual(alignment.annotations["definition"], "Predicted permease") self.assertEqual(alignment.annotations["previous identifier"], "DUF318;") self.assertEqual( alignment.annotations["author"], ["Bateman A;0000-0002-6982-4660"] ) self.assertEqual(alignment.annotations["source of seed"], "COG0701") self.assertEqual(alignment.annotations["gathering method"], "32.30 32.30;") self.assertEqual(alignment.annotations["trusted cutoff"], "32.30 32.40;") self.assertEqual(alignment.annotations["noise cutoff"], "32.20 32.20;") self.assertEqual( alignment.annotations["build method"], "hmmbuild --handHMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual(len(alignment.annotations["nested domains"]), 1) self.assertEqual( alignment.annotations["nested domains"][0]["accession"], "PF04945;" ) self.assertEqual( alignment.annotations["nested domains"][0]["location"], "D4GY01.1/189-231" ) self.assertEqual(len(alignment.annotations["database references"]), 3) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR005524;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "TC; 2.A.119;" ) self.assertEqual( alignment.annotations["database references"][2]["reference"], "SO; 0100021; polypeptide_conserved_region;", ) self.assertEqual( alignment.annotations["comment"], "This family of integral membrane proteins are predicted to be permeases of unknown specificity.", ) self.assertEqual(len(alignment.sequences), 11) self.assertEqual(alignment.sequences[0].id, "O26980_METTH/26-325") self.assertEqual(alignment.sequences[1].id, "O67395_AQUAE/24-315") self.assertEqual(alignment.sequences[2].id, "Q9X092_THEMA/31-364") self.assertEqual(alignment.sequences[3].id, "O28037_ARCFU/7-346") self.assertEqual(alignment.sequences[4].id, "Y584_METJA/16-362") self.assertEqual(alignment.sequences[5].id, "Y2963_MYCTU/18-329") self.assertEqual(alignment.sequences[6].id, "D4GY01_HALVD/35-380") self.assertEqual(alignment.sequences[7].id, "YCGR_BACSU/7-294") self.assertEqual(alignment.sequences[8].id, "Q9KCQ1_BACHD/41-335") self.assertEqual(alignment.sequences[9].id, "P72867_SYNY3/3-335") self.assertEqual(alignment.sequences[10].id, "P73433_SYNY3/6-329") self.assertEqual(alignment.sequences[0].annotations["accession"], "O26980.1") self.assertEqual(alignment.sequences[1].annotations["accession"], "O67395.1") self.assertEqual(alignment.sequences[2].annotations["accession"], "Q9X092.1") self.assertEqual(alignment.sequences[3].annotations["accession"], "O28037.1") self.assertEqual(alignment.sequences[4].annotations["accession"], "Q58004.3") self.assertEqual(alignment.sequences[5].annotations["accession"], "I6YET7.1") self.assertEqual(alignment.sequences[6].annotations["accession"], "D4GY01.1") self.assertEqual(alignment.sequences[7].annotations["accession"], "P94395.1") self.assertEqual(alignment.sequences[8].annotations["accession"], "Q9KCQ1.1") self.assertEqual(alignment.sequences[9].annotations["accession"], "P72867.1") self.assertEqual(alignment.sequences[10].annotations["accession"], "P73433.1") self.assertEqual( alignment.sequences[0].seq, "HLGSAVNFFIYDTIKIFILLATLIFVISFIRTYIPPNKVKETLEKRHRYTGNFIAALVGIITPFCSCSAVPLFIGFVEAGVPLGATFSFLISSPMINEIAIILLLGLFGWQITAFYILSGFIIAVLGGILIGKLKMETELEDYVYETLEKMRALGVADVELPKPTLRERYVIAKNEMKDILRRVSPYIVIAIAIGGWIHGYLPEDFLLQYAGADNIFAVPMAVIIGVPLYSNAAGTIPLISALIEKGMAAGTALALMMSITALSLPEMIILRKVMKPKLLATFIAILAVSITLTGYIFNL", ) self.assertEqual( alignment.sequences[1].seq, "HLAEALHFFVYDTLKIFTLLTVIIFVVSFIRSFFPLEKTREILSKHKAVALPLAAFLGILTPFCSCSAVPMFIGFVEAGIPLGAAFTFLVASPMVNEVALGLLLTLFGVKVAVLYVIFGVIVAIVAGYVIEKLNPRELIADYVFQVKLGQTQIKEMTFKERLEFAKNNVKEILGKIWIYIIIAIGIGGFIHGYVPQDIVERVAKTAGLIAVPLAVLIGIPLYSNAAGILPVIQALIAKGVPLGTALAFMMATTALSFPEFMILKQIMKPKLIAFFAGIVGISIIAVGYLFNF", ) self.assertEqual( alignment.sequences[2].seq, "ILNGFYLLHEYAREHVLLCLVPAFFIAGTISVMLKKDAVLKLLGPNAKRIISYPVAAISGGILAVCSCTILPLFGGIYKKGAGIGPATTFLFAGPAINIAAIFLTARVLGWDLGLARLIATITAAVLIGLIMEMIYQERGEGGLAFTSDDDQYGVRGIIFFLIQLGFLVTSSLGINQTLKYSLMTLLGISALFMALFGFKRDTVENWLYETWDFAKKILPYLFIGVFFAGVLTRLLPQQVVTALLGSNSFLSNLVASVIGTLMYFATLTEVPIVQALRELGMAKGPTLALLMAGNSLSLPSMIVITKLLGKKKAFTYFGLVVVFSTLFGMIYGV", ) self.assertEqual( alignment.sequences[3].seq, "LLAGIQALEEYIALHVLTCLVPAFLIAGALMSMMNKAVLINYLGAATSKLKSFPLAIVSSFFLAVCSCTVIPIASGIYKRTNATAPAMIILWVAPATNILAVTYTGAVLGLELALARIVAAISTAFVVGLILFYVFDRKIASQSDSAMPKAGRLVENNALVLFALLVATLLLPNYLGVGKPYIFKVEVFSVLMLVTTVYALKSFSKEDLKYWMLETWFFVKQIIPLLLVGVFIVGVVGEILKATDVVEVYLGGEGVGQSFLAALIGALSYFATMTEAPFVDTLMKLGMGKGPALALLLAGPGLSLPNMLAIGKLFGVKRAAVYIITIVALSTIAGVVYGE", ) self.assertEqual( alignment.sequences[4].seq, "MINTIIDYLNVNRVLALLMAFLMAGGIASMINKNFIIKYFGSNTPKYISYTVAAVSGSLLAVCSCTILPLFASIYKRGAGIGPATTFLFSGPAINVLAIFYSAALLGWDIGFLRAVFAVVVSILIGLSMEIIFKSHEKKRALRVPKADKISDRPLYQTITFFALQFIMLLVITASPKLFPTLSMPLYDGFLLKHLLFIILGIILAVTTKIWFKDEEIKNWLRESFTLLKIVFPLLIIGVAIAGAIKAIIPPSYIATYVGGNSITANFIASFIGALMYFATLTEVPIIKALMELGMGVGPAMALLLAGPSLSIPTVLTISKVLGKTKALTYLGLVVIFSTICGYIAGI", ) self.assertEqual( alignment.sequences[5].seq, "IGHALALTASMTWEILWALILGFALSAVVQAVVRRSTIVTLLGDDRPRTLVIATGLGAASSSCSYAAVALARSLFRKGANFTAAMAFEIGSTNLVVELGIILALLMGWQFTAAEFVGGPIMILVLAVLFRLFVGARLIDAAREQAERGLAGSMEGHAAMDMSIKREGSFWRRLLSPPGFTSIAHVFVMEWLAILRDLILGLLIAGAIAAWVPESFWQSFFLANHPAWSAVWGPIIGPIVAIVSFVCSIGNVPLAAVLWNGGISFGGVIAFIFADLLILPILNIYRKYYGARMMLVLLGTFYASMVVAGYLIE", ) self.assertEqual( alignment.sequences[6].seq, "SAREALSTTAAMAWVTWWALVVGFAIAGGVEAWTSGEEVSELLEGHGPREIGYGSLFGFVSSSCSYSAIATAKNLFKKGGSAAATLGAFMFASTNLVIEIGAVIWILLGWQFLVADILGGFILIGLMAFGFVYLVPDEVVEQARRNVQDEGSETVRDPVCGMEVDPDETEYSVERDGRTFYFCSKSCKESFDPEEANTTVRERATSLSGWKALADKQWKEWGMLWDEIAIGFVFAGLIAGFIPDAVWTSVFSGPTFGLPVYVFWTAVLGAVIGVATFVCSVGNVPFGAVLFSNGLPFGSVLSYIYADLIVPPIVDAYREYYGTTFAAVLSGMIFVAAVLTGVVIHF", ) self.assertEqual( alignment.sequences[7].seq, "FLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIMPKNRFLAVLFGALAGVLFPACECGIIPITRRLLLKGVPLHAGVAFMLTAPIINPIVLFSTYIAFGNRWSVVFYRGGLALAVSLIIGVILSYQFKDNQLLKPDEPGHHHHHHGTLLQKLGGTLRHAIDEFFSVGKYLIIGAFIAAAMQTYVKTSTLLAIGQNDVSSSLVMMGLAFVLSLCSEVDAFIASSFSSTFSLGSLIAFLVFGAMVDIKNLLMMLAAFKKRFVFLLITYIVVIVLAGSLLVKG", ) self.assertEqual( alignment.sequences[8].seq, "WMNVNTIFLGIVIEAVPFILLGVFVSALIQIYVKEDTIQRYLPKNAYAALLPAAVLGAIFPICECAIVPIVRRLIKKGMPLHVGVVFLVAAPILNPIVAASTYFAFRTDLTVLYARMGLAFILSIVIGGLLYVMFKNSDQLKWTKEELVGRVPVQSDMELKPKMNRLKQTLYHASDEFFLMGKYLIAGAFIAALFQTFLDRNILVTIGSNEWSSTGVMMAFAFILSLCSEADAFVAASFGSTFTTGSLIAFLVYGPMLDLKNTIMLFAFFKSKFVLAFMITVTVVVFLAVMVLQF", ) self.assertEqual( alignment.sequences[9].seq, "QLHEAFTIFLSLLVEAIPFLTFGVVLSSALLVFSDEKKLIAYIPRNPFLGAIAGSLVGFMFPVCECGNVPVARRFLMQGLPPSVAVAFLLAAPTINPIVIWSTWVAFRDQPGMVVARVVCSLIITVIVSWVFSRQLDAVPLLKPALGRRLAYLTRPEESPTAIACESPLLQSGTFLLGSGNSGQLLKLDEQAVETLLPPIAPSRWEMFTDNIVQELRELGGMLILGSLIAAVIQVFIPREWILLLGQGTISSILAMMLLSVVVSVCSTVDSFFALSFVSTFTSSSLLAFLVFGPMIDVKSIGLLLSVFQRRIVIYLLLLTGQLTFLLSLAHSY", ) self.assertEqual( alignment.sequences[10].seq, "EFNLFLDLLGSALLLSLPWLLLGIIISSTFLIWTDEQKWVANFPRNRLLSSLVGSALGFLLPLGAFGSVPLVRRLLLQGAPIPLAVSFLVAAPTLNIFAIVRVLSSRQSQYGLIFLCISCSWLMAIVMGLVFSTYRLARQQAEDEGETALLNIPLLRSGALIILQSSMEASPRQGGLVFASGVNPVADFSWRQKLHLFGRNIIEEFQEFGGVLVIGTAIACGIVFFLPQAWLLQWAGLGPVRQTVLMMGWSFILPLGNFSNPDLLAPLGEQLWRGSMVAFLLWGSLFNLQTIGLWLVTLRLRPLSYLVVLVGLSVFLFAMVTNY", ) self.assertEqual( alignment[0], "HLGSAVNFFIYDTIKIFILLATLIFVISFIRTYIPPNKVKETLE-KRHRYTGNFIAALVGIITPFCSCSAVPLFIGFVEAGVPLGATF-SFLISSPMINEIAIILLLGLFG--WQITAFYILSGFIIAVLGGILIGKLKMETELEDYVYETLE-------------------------KMRALGVADV------------------ELPKPTLR---ERYV--IAKNEMKDILRRVS-------PYIVIAIAIGGWIHGYL-PEDFLLQYA--GADNIF-------AVPMAVIIGVPLYSNAAGTIPLISALIEKGMAAGTALALMMSITALSLPEMIILRKVMKPKLLATFIAILAVSITLTGYIFNL", ) self.assertEqual( alignment[1], "HLAEALHFFVYDTLKIFTLLTVIIFVVSFIRSFFPLEKTREIL--SKHKAVALPLAAFLGILTPFCSCSAVPMFIGFVEAGIPLGAAF-TFLVASPMVNEVALGLLLTLFG--VKVAVLYVIFGVIVAIVAGYVIEKLNPRELIADYVFQV---------------------------KLGQTQIKEM-------------------TFKERLE---------FAKNNVKEILGKIW-------IYIIIAIGIGGFIHGYV-PQDIVERVA--KTAGLI-------AVPLAVLIGIPLYSNAAGILPVIQALIAKGVPLGTALAFMMATTALSFPEFMILKQIMKPKLIAFFAGIVGISIIAVGYLFNF", ) self.assertEqual( alignment[2], "ILNGFYLLHEYAREHVLLCLVPAFFIAGTISVMLKKDAVLKLLGPNAKRIISYPVAAISGGILAVCSCTILPLFGGIYKKGAGIGPAT-TFLFAGPAINIAAIFLTARVLG--WDLGLARLIATITAAVLIGLIMEMIYQERGEGGLAFTSDD-----DQYGVRGIIFFLIQLG--FLVTSSLGINQTLKYS----------LMTLLGISALFM---ALFG--FKRDTVENWLYETWDFAKKILPYLFIGVFFAGVLTRLL-PQQVVTALL--GSNSFL-------SNLVASVIGTLMYFATLTEVPIVQALRELGMAKGPTLALLMAGNSLSLPSMIVITKLLGKKKAFTYFGLVVVFSTLFGMIYGV", ) self.assertEqual( alignment[3], "LLAGIQALEEYIALHVLTCLVPAFLIAGALMSMMNKAVLINYLGAATSKLKSFPLAIVSSFFLAVCSCTVIPIASGIYKRTNATAPAM-IILWVAPATNILAVTYTGAVLG--LELALARIVAAISTAFVVGLILFYVFDRKIASQSDSAMPKAGRLVEN---NALVLFALLVAT-LLLPNYLGVGKPYIFKV--------EVFSVLMLVTTVY---ALKS--FSKEDLKYWMLETWFFVKQIIPLLLVGVFIVGVVGEILKATDVVEVYL--GGEGVG-------QSFLAALIGALSYFATMTEAPFVDTLMKLGMGKGPALALLLAGPGLSLPNMLAIGKLFGVKRAAVYIITIVALSTIAGVVYGE", ) self.assertEqual( alignment[4], "---MINTIIDYLNVNRVLALLMAFLMAGGIASMINKNFIIKYFGSNTPKYISYTVAAVSGSLLAVCSCTILPLFASIYKRGAGIGPAT-TFLFSGPAINVLAIFYSAALLG--WDIGFLRAVFAVVVSILIGLSMEIIFKSHEKKRALR-VPKADKISDRPLYQTITFFALQFIMLLVITASPKLFPTLSMPLYDGFLLKHLLFIILGIILAVT---TKIW--FKDEEIKNWLRESFTLLKIVFPLLIIGVAIAGAIKAII-PPSYIATYV--GGNSIT-------ANFIASFIGALMYFATLTEVPIIKALMELGMGVGPAMALLLAGPSLSIPTVLTISKVLGKTKALTYLGLVVIFSTICGYIAGI", ) self.assertEqual( alignment[5], "-IGHALALTASMTWEILWALILGFALSAVVQAVVRRSTIVTLLGDDRPR--TLVIATGLGAASSSCSYAAVALARSLFRKGANFTAAM-AFEIGSTNLVVELGIILALLMG--WQFTAAEFVGGPIMILVLAVLF-RLFVGARLIDAAREQAERGLAGSMEGHAAMDMS---------IKREGSFWRR------------------LLSPPGFT---S-----IAHVFVMEW-LAIL-------RDLILGLLIAGAIAAWV-PESFWQSFFLANHPAWSA----VWGPIIGPIVAIVSFVCSIGNVPLAAVLWNGGISFGGVIAF-IFADLLILPILNIYRKYYGARMMLVLLGTFYASMVVAGYLIE-", ) self.assertEqual( alignment[6], "SAREALSTTAAMAWVTWWALVVGFAIAGGVEAWTSGEEVSELLEGHGPREIGY--GSLFGFVSSSCSYSAIATAKNLFKKGGSAAATLGAFMFASTNLVIEIGAVIWILLG--WQFLVADILGGFILIGLMAFGFVYLVPDEVVEQARRNVQDEGSETVRDPVCGMEVDPDETE--YSVERDGRTFYFCSKSCKESFDPEEANTTVRERATSLS---GWKA--LADKQWKEW-GMLW-------DEIAIGFVFAGLIAGFI-PDAVWTSVF--SGPTFGLPVYVFWTAVLGAVIGVATFVCSVGNVPFGAVLFSNGLPFGSVLSY-IYADLIVPPIVDAYREYYGTTFAAVLSGMIFVAAVLTGVVIHF", ) self.assertEqual( alignment[7], "-FLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIM--PKNRFLAVLFGALAGVLFPACECGIIPITRRLLLKGVPLHAGV-AFMLTAPIINPIVLFSTYIAFGNRWSVVFYRGGLALAVSLIIGVILSYQFKDNQLLKPD------------------------------EPGHHHHHHG-------------------TLLQKLG---G-----TLRHAIDEF-FSVG-------KYLIIGAFIAAAMQTYV-KTSTLLAI---GQNDVS-------SSLVMMGLAFVLSLCSEVD-AFIASSFSSTFSLGSLIAFLVFGAMVDIKNLLMMLAAFKKRFVFLLITYIVVIVLAGSLLVKG", ) self.assertEqual( alignment[8], "-WMNVNTIFLGIVIEAVPFILLGVFVSALIQIYVKEDTIQRYL--PKNAYAALLPAAVLGAIFPICECAIVPIVRRLIKKGMPLHVGV-VFLVAAPILNPIVAASTYFAFRTDLTVLYARMGLAFILSIVIGGLLYVMFKNSDQLKWTKEE---------------------------LVGRVPVQSD------------------MELKPKMN---RLKQ--TLYHASDEF-FLMG-------KYLIAGAFIAALFQTFL-DRNILVTI---GSNEWS-------STGVMMAFAFILSLCSEAD-AFVAASFGSTFTTGSLIAFLVYGPMLDLKNTIMLFAFFKSKFVLAFMITVTVVVFLAVMVLQF", ) self.assertEqual( alignment[9], "QLHEAFTIFLSLLVEAIPFLTFGVVLSSALLVFSDEKKLIAYI--PRNPFLGAIAGSLVGFMFPVCECGNVPVARRFLMQGLPPSVAV-AFLLAAPTINPIVIWSTWVAFRDQPGMVVARVVCSLIITVIVSWVFSRQLDAVPLLKPALGRRLAYLTRPEESPTAIACESPLLQSGTFLLGSGNSGQLLKLD----------EQAVETLLPPIA---PSRWEMFTDNIVQEL-RELG-------GMLILGSLIAAVIQVFI-PREWILLL---GQGTIS-------SILAMMLLSVVVSVCSTVD-SFFALSFVSTFTSSSLLAFLVFGPMIDVKSIGLLLSVFQRRIVIYLLLLTGQLTFLLSLAHSY", ) self.assertEqual( alignment[10], "EFNLFLDLLGSALLLSLPWLLLGIIISSTFLIWTDEQKWVANF--PRNRLLSSLVGSALGFLLPLGAFGSVPLVRRLLLQGAPIPLAV-SFLVAAPTLNIFAIVRVLSSRQSQYGLIFLCISCSWLMAIVMGLVFSTYRLARQQAEDEGETALLNIPLLRSGALIILQSSMEA-----SPRQGGLVFA------------------SGVNPVADFSWRQKLHLFGRNIIEEF-QEFG-------GVLVIGTAIACGIVFFL-PQAWLLQWA--GLGPVR-------QTVLMMGWSFILPLGNFSN-PDLLAPLGEQLWRGSMVAFLLWGSLFNLQTIGLWLVTLRLRPLSYLVVLVGLSVFLFAMVTNY", ) self.assertEqual( alignment.column_annotations["consensus sequence"], ".htphhslhhhhslcslhhLlhuhhluuslpsahscpplhchL..s+s+hluhhlAulhGhlhssCSCuslPlspslhc+GsslusAh.sFLluuPslN.lslhhshhlhG..aplshhcllsuhllulllGllhthlh.spthtcsshph.............hh............lhspssltps...................tlhssls...s.h...hs+ptlcEa.hchh.......shLlIGshIAGsIpsal.Ppshlhshh..Gsssls.......ushluslluhlhahsohsshPhlsuLhspGhshGoslAaLlhGshLslPshhhltphhtt+hshshlshlslhshlsGhlhsh", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxxx...xxxx..xxxxxxxxx.xxxx.......xxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 0, 1, 3, 43, 44, 44, 48, 50, 52, 54, 87, 87, 109, 109, 131, 132, 144, 145, 146, 147, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 159, 159, 159, 159, 159, 159, 160, 167, 167, 168, 171, 171, 180, 181, 185, 185, 202, 202, 210, 211, 211, 217, 217, 217, 217, 236, 237, 256, 257, 299, 300], [ 0, 1, 3, 43, 43, 43, 47, 49, 51, 53, 86, 86, 108, 108, 130, 131, 143, 144, 145, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 156, 156, 156, 156, 156, 156, 156, 163, 163, 163, 163, 163, 172, 173, 177, 177, 194, 194, 202, 203, 203, 209, 209, 209, 209, 228, 229, 248, 249, 291, 292], [ 0, 1, 3, 43, 44, 45, 49, 51, 53, 55, 88, 88, 110, 110, 132, 133, 145, 146, 147, 148, 150, 150, 152, 155, 161, 165, 166, 166, 166, 168, 178, 182, 182, 182, 182, 186, 187, 194, 194, 195, 198, 198, 207, 208, 212, 219, 236, 236, 244, 245, 245, 251, 251, 251, 251, 270, 271, 290, 291, 333, 334], [ 0, 1, 3, 43, 44, 45, 49, 51, 53, 55, 88, 88, 110, 110, 132, 133, 145, 146, 147, 148, 150, 155, 157, 157, 163, 167, 168, 169, 169, 171, 181, 185, 186, 186, 187, 191, 192, 199, 199, 200, 203, 203, 212, 213, 217, 224, 241, 242, 250, 251, 251, 257, 257, 257, 257, 276, 277, 296, 297, 339, 340], [ 0, 0, 0, 40, 41, 42, 46, 48, 50, 52, 85, 85, 107, 107, 129, 130, 142, 143, 143, 144, 146, 151, 153, 156, 162, 166, 167, 168, 169, 171, 181, 185, 186, 194, 195, 199, 200, 207, 207, 208, 211, 211, 220, 221, 225, 232, 249, 249, 257, 258, 258, 264, 264, 264, 264, 283, 284, 303, 304, 346, 347], [ 0, 0, 2, 42, 43, 44, 48, 48, 50, 52, 85, 85, 107, 107, 129, 129, 141, 142, 143, 144, 146, 151, 153, 156, 162, 162, 162, 162, 162, 162, 172, 172, 172, 172, 172, 172, 173, 180, 180, 181, 181, 181, 190, 190, 194, 194, 211, 211, 219, 220, 222, 228, 229, 229, 231, 250, 251, 270, 270, 312, 312], [ 0, 1, 3, 43, 44, 45, 49, 51, 53, 53, 86, 87, 109, 109, 131, 132, 144, 145, 146, 147, 149, 154, 156, 159, 165, 169, 170, 170, 170, 172, 182, 186, 187, 195, 196, 200, 201, 208, 208, 209, 212, 212, 221, 221, 225, 225, 242, 242, 250, 251, 251, 257, 258, 262, 264, 283, 284, 303, 303, 345, 346], [ 0, 0, 2, 42, 42, 42, 46, 48, 50, 52, 85, 85, 107, 109, 131, 132, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 154, 154, 154, 154, 154, 154, 154, 161, 161, 162, 162, 162, 171, 171, 175, 175, 192, 192, 200, 200, 200, 206, 206, 206, 206, 225, 225, 244, 245, 287, 288], [ 0, 0, 2, 42, 42, 42, 46, 48, 50, 52, 85, 85, 107, 109, 131, 132, 144, 145, 146, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 157, 157, 157, 157, 157, 157, 158, 165, 165, 166, 169, 169, 178, 178, 182, 182, 199, 199, 207, 207, 207, 213, 213, 213, 213, 232, 232, 251, 252, 294, 295], [ 0, 1, 3, 43, 43, 43, 47, 49, 51, 53, 86, 86, 108, 110, 132, 133, 145, 146, 147, 148, 150, 155, 157, 160, 166, 170, 171, 172, 173, 175, 185, 189, 189, 189, 189, 193, 194, 201, 201, 202, 205, 207, 216, 216, 220, 220, 237, 237, 245, 245, 245, 251, 251, 251, 251, 270, 270, 289, 290, 332, 333], [ 0, 1, 3, 43, 43, 43, 47, 49, 51, 53, 86, 86, 108, 110, 132, 133, 145, 146, 147, 148, 150, 155, 157, 160, 166, 170, 170, 170, 170, 170, 180, 180, 180, 180, 180, 180, 181, 188, 191, 192, 195, 197, 206, 206, 210, 210, 227, 227, 235, 236, 236, 242, 242, 242, 242, 261, 261, 280, 281, 323, 324] ] # fmt: on ), ) ) self.assertEqual( str(alignment), """\ O26980_ME 0 HLGSAVNFFIYDTIKIFILLATLIFVISFIRTYIPPNKVKETLE-KRHRYTGNFIAALVG O67395_AQ 0 HLAEALHFFVYDTLKIFTLLTVIIFVVSFIRSFFPLEKTREIL--SKHKAVALPLAAFLG Q9X092_TH 0 ILNGFYLLHEYAREHVLLCLVPAFFIAGTISVMLKKDAVLKLLGPNAKRIISYPVAAISG O28037_AR 0 LLAGIQALEEYIALHVLTCLVPAFLIAGALMSMMNKAVLINYLGAATSKLKSFPLAIVSS Y584_METJ 0 ---MINTIIDYLNVNRVLALLMAFLMAGGIASMINKNFIIKYFGSNTPKYISYTVAAVSG Y2963_MYC 0 -IGHALALTASMTWEILWALILGFALSAVVQAVVRRSTIVTLLGDDRPR--TLVIATGLG D4GY01_HA 0 SAREALSTTAAMAWVTWWALVVGFAIAGGVEAWTSGEEVSELLEGHGPREIGY--GSLFG YCGR_BACS 0 -FLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIM--PKNRFLAVLFGALAG Q9KCQ1_BA 0 -WMNVNTIFLGIVIEAVPFILLGVFVSALIQIYVKEDTIQRYL--PKNAYAALLPAAVLG P72867_SY 0 QLHEAFTIFLSLLVEAIPFLTFGVVLSSALLVFSDEKKLIAYI--PRNPFLGAIAGSLVG P73433_SY 0 EFNLFLDLLGSALLLSLPWLLLGIIISSTFLIWTDEQKWVANF--PRNRLLSSLVGSALG O26980_ME 59 IITPFCSCSAVPLFIGFVEAGVPLGATF-SFLISSPMINEIAIILLLGLFG--WQITAFY O67395_AQ 58 ILTPFCSCSAVPMFIGFVEAGIPLGAAF-TFLVASPMVNEVALGLLLTLFG--VKVAVLY Q9X092_TH 60 GILAVCSCTILPLFGGIYKKGAGIGPAT-TFLFAGPAINIAAIFLTARVLG--WDLGLAR O28037_AR 60 FFLAVCSCTVIPIASGIYKRTNATAPAM-IILWVAPATNILAVTYTGAVLG--LELALAR Y584_METJ 57 SLLAVCSCTILPLFASIYKRGAGIGPAT-TFLFSGPAINVLAIFYSAALLG--WDIGFLR Y2963_MYC 57 AASSSCSYAAVALARSLFRKGANFTAAM-AFEIGSTNLVVELGIILALLMG--WQFTAAE D4GY01_HA 58 FVSSSCSYSAIATAKNLFKKGGSAAATLGAFMFASTNLVIEIGAVIWILLG--WQFLVAD YCGR_BACS 57 VLFPACECGIIPITRRLLLKGVPLHAGV-AFMLTAPIINPIVLFSTYIAFGNRWSVVFYR Q9KCQ1_BA 57 AIFPICECAIVPIVRRLIKKGMPLHVGV-VFLVAAPILNPIVAASTYFAFRTDLTVLYAR P72867_SY 58 FMFPVCECGNVPVARRFLMQGLPPSVAV-AFLLAAPTINPIVIWSTWVAFRDQPGMVVAR P73433_SY 58 FLLPLGAFGSVPLVRRLLLQGAPIPLAV-SFLVAAPTLNIFAIVRVLSSRQSQYGLIFLC O26980_ME 116 ILSGFIIAVLGGILIGKLKMETELEDYVYETLE-------------------------KM O67395_AQ 115 VIFGVIVAIVAGYVIEKLNPRELIADYVFQV---------------------------KL Q9X092_TH 117 LIATITAAVLIGLIMEMIYQERGEGGLAFTSDD-----DQYGVRGIIFFLIQLG--FLVT O28037_AR 117 IVAAISTAFVVGLILFYVFDRKIASQSDSAMPKAGRLVEN---NALVLFALLVAT-LLLP Y584_METJ 114 AVFAVVVSILIGLSMEIIFKSHEKKRALR-VPKADKISDRPLYQTITFFALQFIMLLVIT Y2963_MYC 114 FVGGPIMILVLAVLF-RLFVGARLIDAAREQAERGLAGSMEGHAAMDMS---------IK D4GY01_HA 116 ILGGFILIGLMAFGFVYLVPDEVVEQARRNVQDEGSETVRDPVCGMEVDPDETE--YSVE YCGR_BACS 116 GGLALAVSLIIGVILSYQFKDNQLLKPD------------------------------EP Q9KCQ1_BA 116 MGLAFILSIVIGGLLYVMFKNSDQLKWTKEE---------------------------LV P72867_SY 117 VVCSLIITVIVSWVFSRQLDAVPLLKPALGRRLAYLTRPEESPTAIACESPLLQSGTFLL P73433_SY 117 ISCSWLMAIVMGLVFSTYRLARQQAEDEGETALLNIPLLRSGALIILQSSMEA-----SP O26980_ME 151 RALGVADV------------------ELPKPTLR---ERYV--IAKNEMKDILRRVS--- O67395_AQ 148 GQTQIKEM-------------------TFKERLE---------FAKNNVKEILGKIW--- Q9X092_TH 170 SSLGINQTLKYS----------LMTLLGISALFM---ALFG--FKRDTVENWLYETWDFA O28037_AR 173 NYLGVGKPYIFKV--------EVFSVLMLVTTVY---ALKS--FSKEDLKYWMLETWFFV Y584_METJ 173 ASPKLFPTLSMPLYDGFLLKHLLFIILGIILAVT---TKIW--FKDEEIKNWLRESFTLL Y2963_MYC 164 REGSFWRR------------------LLSPPGFT---S-----IAHVFVMEW-LAIL--- D4GY01_HA 174 RDGRTFYFCSKSCKESFDPEEANTTVRERATSLS---GWKA--LADKQWKEW-GMLW--- YCGR_BACS 146 GHHHHHHG-------------------TLLQKLG---G-----TLRHAIDEF-FSVG--- Q9KCQ1_BA 149 GRVPVQSD------------------MELKPKMN---RLKQ--TLYHASDEF-FLMG--- P72867_SY 177 GSGNSGQLLKLD----------EQAVETLLPPIA---PSRWEMFTDNIVQEL-RELG--- P73433_SY 172 RQGGLVFA------------------SGVNPVADFSWRQKLHLFGRNIIEEF-QEFG--- O26980_ME 185 ----PYIVIAIAIGGWIHGYL-PEDFLLQYA--GADNIF-------AVPMAVIIGVPLYS O67395_AQ 177 ----IYIIIAIGIGGFIHGYV-PQDIVERVA--KTAGLI-------AVPLAVLIGIPLYS Q9X092_TH 215 KKILPYLFIGVFFAGVLTRLL-PQQVVTALL--GSNSFL-------SNLVASVIGTLMYF O28037_AR 220 KQIIPLLLVGVFIVGVVGEILKATDVVEVYL--GGEGVG-------QSFLAALIGALSYF Y584_METJ 228 KIVFPLLIIGVAIAGAIKAII-PPSYIATYV--GGNSIT-------ANFIASFIGALMYF Y2963_MYC 194 ----RDLILGLLIAGAIAAWV-PESFWQSFFLANHPAWSA----VWGPIIGPIVAIVSFV D4GY01_HA 225 ----DEIAIGFVFAGLIAGFI-PDAVWTSVF--SGPTFGLPVYVFWTAVLGAVIGVATFV YCGR_BACS 175 ----KYLIIGAFIAAAMQTYV-KTSTLLAI---GQNDVS-------SSLVMMGLAFVLSL Q9KCQ1_BA 182 ----KYLIAGAFIAALFQTFL-DRNILVTI---GSNEWS-------STGVMMAFAFILSL P72867_SY 220 ----GMLILGSLIAAVIQVFI-PREWILLL---GQGTIS-------SILAMMLLSVVVSV P73433_SY 210 ----GVLVIGTAIACGIVFFL-PQAWLLQWA--GLGPVR-------QTVLMMGWSFILPL O26980_ME 231 NAAGTIPLISALIEKGMAAGTALALMMSITALSLPEMIILRKVMKPKLLATFIAILAVSI O67395_AQ 223 NAAGILPVIQALIAKGVPLGTALAFMMATTALSFPEFMILKQIMKPKLIAFFAGIVGISI Q9X092_TH 265 ATLTEVPIVQALRELGMAKGPTLALLMAGNSLSLPSMIVITKLLGKKKAFTYFGLVVVFS O28037_AR 271 ATMTEAPFVDTLMKLGMGKGPALALLLAGPGLSLPNMLAIGKLFGVKRAAVYIITIVALS Y584_METJ 278 ATLTEVPIIKALMELGMGVGPAMALLLAGPSLSIPTVLTISKVLGKTKALTYLGLVVIFS Y2963_MYC 245 CSIGNVPLAAVLWNGGISFGGVIAF-IFADLLILPILNIYRKYYGARMMLVLLGTFYASM D4GY01_HA 278 CSVGNVPFGAVLFSNGLPFGSVLSY-IYADLIVPPIVDAYREYYGTTFAAVLSGMIFVAA YCGR_BACS 220 CSEVD-AFIASSFSSTFSLGSLIAFLVFGAMVDIKNLLMMLAAFKKRFVFLLITYIVVIV Q9KCQ1_BA 227 CSEAD-AFVAASFGSTFTTGSLIAFLVYGPMLDLKNTIMLFAFFKSKFVLAFMITVTVVV P72867_SY 265 CSTVD-SFFALSFVSTFTSSSLLAFLVFGPMIDVKSIGLLLSVFQRRIVIYLLLLTGQLT P73433_SY 256 GNFSN-PDLLAPLGEQLWRGSMVAFLLWGSLFNLQTIGLWLVTLRLRPLSYLVVLVGLSV O26980_ME 291 TLTGYIFNL 300 O67395_AQ 283 IAVGYLFNF 292 Q9X092_TH 325 TLFGMIYGV 334 O28037_AR 331 TIAGVVYGE 340 Y584_METJ 338 TICGYIAGI 347 Y2963_MYC 304 VVAGYLIE- 312 D4GY01_HA 337 VLTGVVIHF 346 YCGR_BACS 279 LAGSLLVKG 288 Q9KCQ1_BA 286 FLAVMVLQF 295 P72867_SY 324 FLLSLAHSY 333 P73433_SY 315 FLFAMVTNY 324 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID ArsP_1 #=GF AC PF03773.15 #=GF DE Predicted permease #=GF AU Bateman A;0000-0002-6982-4660 #=GF SE COG0701 #=GF GA 32.30 32.30; #=GF TC 32.30 32.40; #=GF NC 32.20 32.20; #=GF BM hmmbuild --handHMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF PI DUF318; #=GF NE PF04945; #=GF NL D4GY01.1/189-231 #=GF DR INTERPRO; IPR005524; #=GF DR TC; 2.A.119; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC This family of integral membrane proteins are predicted to be #=GF CC permeases of unknown specificity. #=GF SQ 11 #=GS O26980_METTH/26-325 AC O26980.1 #=GS O67395_AQUAE/24-315 AC O67395.1 #=GS Q9X092_THEMA/31-364 AC Q9X092.1 #=GS O28037_ARCFU/7-346 AC O28037.1 #=GS Y584_METJA/16-362 AC Q58004.3 #=GS Y2963_MYCTU/18-329 AC I6YET7.1 #=GS D4GY01_HALVD/35-380 AC D4GY01.1 #=GS YCGR_BACSU/7-294 AC P94395.1 #=GS Q9KCQ1_BACHD/41-335 AC Q9KCQ1.1 #=GS P72867_SYNY3/3-335 AC P72867.1 #=GS P73433_SYNY3/6-329 AC P73433.1 O26980_METTH/26-325 HLGSAVNFFIYDTIKIFILLATLIFVISFIRTYIPPNKVKETLE.KRHRYTGNFIAALVGIITPFCSCSAVPLFIGFVEAGVPLGATF.SFLISSPMINEIAIILLLGLFG..WQITAFYILSGFIIAVLGGILIGKLKMETELEDYVYETLE.........................KMRALGVADV..................ELPKPTLR...ERYV..IAKNEMKDILRRVS.......PYIVIAIAIGGWIHGYL.PEDFLLQYA..GADNIF.......AVPMAVIIGVPLYSNAAGTIPLISALIEKGMAAGTALALMMSITALSLPEMIILRKVMKPKLLATFIAILAVSITLTGYIFNL O67395_AQUAE/24-315 HLAEALHFFVYDTLKIFTLLTVIIFVVSFIRSFFPLEKTREIL..SKHKAVALPLAAFLGILTPFCSCSAVPMFIGFVEAGIPLGAAF.TFLVASPMVNEVALGLLLTLFG..VKVAVLYVIFGVIVAIVAGYVIEKLNPRELIADYVFQV...........................KLGQTQIKEM...................TFKERLE.........FAKNNVKEILGKIW.......IYIIIAIGIGGFIHGYV.PQDIVERVA..KTAGLI.......AVPLAVLIGIPLYSNAAGILPVIQALIAKGVPLGTALAFMMATTALSFPEFMILKQIMKPKLIAFFAGIVGISIIAVGYLFNF Q9X092_THEMA/31-364 ILNGFYLLHEYAREHVLLCLVPAFFIAGTISVMLKKDAVLKLLGPNAKRIISYPVAAISGGILAVCSCTILPLFGGIYKKGAGIGPAT.TFLFAGPAINIAAIFLTARVLG..WDLGLARLIATITAAVLIGLIMEMIYQERGEGGLAFTSDD.....DQYGVRGIIFFLIQLG..FLVTSSLGINQTLKYS..........LMTLLGISALFM...ALFG..FKRDTVENWLYETWDFAKKILPYLFIGVFFAGVLTRLL.PQQVVTALL..GSNSFL.......SNLVASVIGTLMYFATLTEVPIVQALRELGMAKGPTLALLMAGNSLSLPSMIVITKLLGKKKAFTYFGLVVVFSTLFGMIYGV O28037_ARCFU/7-346 LLAGIQALEEYIALHVLTCLVPAFLIAGALMSMMNKAVLINYLGAATSKLKSFPLAIVSSFFLAVCSCTVIPIASGIYKRTNATAPAM.IILWVAPATNILAVTYTGAVLG..LELALARIVAAISTAFVVGLILFYVFDRKIASQSDSAMPKAGRLVEN...NALVLFALLVAT.LLLPNYLGVGKPYIFKV........EVFSVLMLVTTVY...ALKS..FSKEDLKYWMLETWFFVKQIIPLLLVGVFIVGVVGEILKATDVVEVYL..GGEGVG.......QSFLAALIGALSYFATMTEAPFVDTLMKLGMGKGPALALLLAGPGLSLPNMLAIGKLFGVKRAAVYIITIVALSTIAGVVYGE Y584_METJA/16-362 ...MINTIIDYLNVNRVLALLMAFLMAGGIASMINKNFIIKYFGSNTPKYISYTVAAVSGSLLAVCSCTILPLFASIYKRGAGIGPAT.TFLFSGPAINVLAIFYSAALLG..WDIGFLRAVFAVVVSILIGLSMEIIFKSHEKKRALR.VPKADKISDRPLYQTITFFALQFIMLLVITASPKLFPTLSMPLYDGFLLKHLLFIILGIILAVT...TKIW..FKDEEIKNWLRESFTLLKIVFPLLIIGVAIAGAIKAII.PPSYIATYV..GGNSIT.......ANFIASFIGALMYFATLTEVPIIKALMELGMGVGPAMALLLAGPSLSIPTVLTISKVLGKTKALTYLGLVVIFSTICGYIAGI Y2963_MYCTU/18-329 .IGHALALTASMTWEILWALILGFALSAVVQAVVRRSTIVTLLGDDRPR..TLVIATGLGAASSSCSYAAVALARSLFRKGANFTAAM.AFEIGSTNLVVELGIILALLMG..WQFTAAEFVGGPIMILVLAVLF.RLFVGARLIDAAREQAERGLAGSMEGHAAMDMS.........IKREGSFWRR..................LLSPPGFT...S.....IAHVFVMEW.LAIL.......RDLILGLLIAGAIAAWV.PESFWQSFFLANHPAWSA....VWGPIIGPIVAIVSFVCSIGNVPLAAVLWNGGISFGGVIAF.IFADLLILPILNIYRKYYGARMMLVLLGTFYASMVVAGYLIE. D4GY01_HALVD/35-380 SAREALSTTAAMAWVTWWALVVGFAIAGGVEAWTSGEEVSELLEGHGPREIGY..GSLFGFVSSSCSYSAIATAKNLFKKGGSAAATLGAFMFASTNLVIEIGAVIWILLG..WQFLVADILGGFILIGLMAFGFVYLVPDEVVEQARRNVQDEGSETVRDPVCGMEVDPDETE..YSVERDGRTFYFCSKSCKESFDPEEANTTVRERATSLS...GWKA..LADKQWKEW.GMLW.......DEIAIGFVFAGLIAGFI.PDAVWTSVF..SGPTFGLPVYVFWTAVLGAVIGVATFVCSVGNVPFGAVLFSNGLPFGSVLSY.IYADLIVPPIVDAYREYYGTTFAAVLSGMIFVAAVLTGVVIHF YCGR_BACSU/7-294 .FLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIM..PKNRFLAVLFGALAGVLFPACECGIIPITRRLLLKGVPLHAGV.AFMLTAPIINPIVLFSTYIAFGNRWSVVFYRGGLALAVSLIIGVILSYQFKDNQLLKPD..............................EPGHHHHHHG...................TLLQKLG...G.....TLRHAIDEF.FSVG.......KYLIIGAFIAAAMQTYV.KTSTLLAI...GQNDVS.......SSLVMMGLAFVLSLCSEVD.AFIASSFSSTFSLGSLIAFLVFGAMVDIKNLLMMLAAFKKRFVFLLITYIVVIVLAGSLLVKG Q9KCQ1_BACHD/41-335 .WMNVNTIFLGIVIEAVPFILLGVFVSALIQIYVKEDTIQRYL..PKNAYAALLPAAVLGAIFPICECAIVPIVRRLIKKGMPLHVGV.VFLVAAPILNPIVAASTYFAFRTDLTVLYARMGLAFILSIVIGGLLYVMFKNSDQLKWTKEE...........................LVGRVPVQSD..................MELKPKMN...RLKQ..TLYHASDEF.FLMG.......KYLIAGAFIAALFQTFL.DRNILVTI...GSNEWS.......STGVMMAFAFILSLCSEAD.AFVAASFGSTFTTGSLIAFLVYGPMLDLKNTIMLFAFFKSKFVLAFMITVTVVVFLAVMVLQF P72867_SYNY3/3-335 QLHEAFTIFLSLLVEAIPFLTFGVVLSSALLVFSDEKKLIAYI..PRNPFLGAIAGSLVGFMFPVCECGNVPVARRFLMQGLPPSVAV.AFLLAAPTINPIVIWSTWVAFRDQPGMVVARVVCSLIITVIVSWVFSRQLDAVPLLKPALGRRLAYLTRPEESPTAIACESPLLQSGTFLLGSGNSGQLLKLD..........EQAVETLLPPIA...PSRWEMFTDNIVQEL.RELG.......GMLILGSLIAAVIQVFI.PREWILLL...GQGTIS.......SILAMMLLSVVVSVCSTVD.SFFALSFVSTFTSSSLLAFLVFGPMIDVKSIGLLLSVFQRRIVIYLLLLTGQLTFLLSLAHSY P73433_SYNY3/6-329 EFNLFLDLLGSALLLSLPWLLLGIIISSTFLIWTDEQKWVANF..PRNRLLSSLVGSALGFLLPLGAFGSVPLVRRLLLQGAPIPLAV.SFLVAAPTLNIFAIVRVLSSRQSQYGLIFLCISCSWLMAIVMGLVFSTYRLARQQAEDEGETALLNIPLLRSGALIILQSSMEA.....SPRQGGLVFA..................SGVNPVADFSWRQKLHLFGRNIIEEF.QEFG.......GVLVIGTAIACGIVFFL.PQAWLLQWA..GLGPVR.......QTVLMMGWSFILPLGNFSN.PDLLAPLGEQLWRGSMVAFLLWGSLFNLQTIGLWLVTLRLRPLSYLVVLVGLSVFLFAMVTNY #=GC seq_cons .htphhslhhhhslcslhhLlhuhhluuslpsahscpplhchL..s+s+hluhhlAulhGhlhssCSCuslPlspslhc+GsslusAh.sFLluuPslN.lslhhshhlhG..aplshhcllsuhllulllGllhthlh.spthtcsshph.............hh............lhspssltps...................tlhssls...s.h...hs+ptlcEa.hchh.......shLlIGshIAGsIpsal.Ppshlhshh..Gsssls.......ushluslluhlhahsohsshPhlsuLhspGhshGoslAaLlhGshLslPshhhltphhtt+hshshlshlslhshlsGhlhsh #=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxxx...xxxx..xxxxxxxxx.xxxx.......xxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx // """, ) def check_alignment_pfam6(self, alignment): """Check the alignment obtained by parsing Pfam record COX2_TM.""" self.assertEqual(alignment.annotations["identifier"], "COX2_TM") self.assertEqual(alignment.annotations["accession"], "PF02790.17") self.assertEqual( alignment.annotations["definition"], "Cytochrome C oxidase subunit II, transmembrane domain", ) self.assertEqual(len(alignment.annotations["author"]), 2) self.assertEqual( alignment.annotations["author"][0], "Sonnhammer ELL;0000-0002-9015-5588" ) self.assertEqual( alignment.annotations["author"][1], "Griffiths-Jones SR;0000-0001-6043-807X" ) self.assertEqual(alignment.annotations["source of seed"], "Prosite") self.assertEqual(alignment.annotations["gathering method"], "22.80 18.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "22.80 21.40;") self.assertEqual(alignment.annotations["noise cutoff"], "22.70 17.90;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual( alignment.annotations["wikipedia"], ["Cytochrome_c_oxidase_subunit_II"] ) self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "8638158") self.assertEqual( alignment.annotations["references"][0]["title"], "The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S;", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Science 1996;272:1136-1144.", ) self.assertEqual(len(alignment.annotations["database references"]), 5) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR011759;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "PROSITE; PDOC00075;", ) self.assertEqual( alignment.annotations["database references"][2]["reference"], "SCOP; 1occ; fa;", ) self.assertEqual( alignment.annotations["database references"][2]["comment"], "This family corresponds to chains b and o.", ) self.assertEqual( alignment.annotations["database references"][3]["reference"], "TC; 3.D.4;" ) self.assertEqual( alignment.annotations["database references"][4]["reference"], "SO; 0100021; polypeptide_conserved_region;", ) self.assertEqual( alignment.annotations["comment"], "The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices.", ) self.assertEqual(len(alignment.sequences), 11) self.assertEqual(alignment.sequences[0].id, "COX2_SCHPO/11-99") self.assertEqual(alignment.sequences[1].id, "COX2_CANGA/17-103") self.assertEqual(alignment.sequences[2].id, "COX2_NEUCR/14-102") self.assertEqual(alignment.sequences[3].id, "H9D0Q0_EMENI/15-102") self.assertEqual(alignment.sequences[4].id, "COX2_ARATH/17-103") self.assertEqual(alignment.sequences[5].id, "COX2_ANOGA/1-83") self.assertEqual(alignment.sequences[6].id, "COX2_CHICK/1-82") self.assertEqual(alignment.sequences[7].id, "COX2_SHEEP/1-83") self.assertEqual(alignment.sequences[8].id, "COX2_STRPU/1-83") self.assertEqual(alignment.sequences[9].id, "COX2_SYNY3/19-111") self.assertEqual(alignment.sequences[10].id, "A1BA41_PARDP/42-128") self.assertEqual(alignment.sequences[0].annotations["accession"], "P21534.4") self.assertEqual(alignment.sequences[1].annotations["accession"], "P43373.2") self.assertEqual(alignment.sequences[2].annotations["accession"], "P00411.2") self.assertEqual(alignment.sequences[3].annotations["accession"], "H9D0Q0.1") self.assertEqual(alignment.sequences[4].annotations["accession"], "P93285.2") self.assertEqual(alignment.sequences[5].annotations["accession"], "P34840.1") self.assertEqual(alignment.sequences[6].annotations["accession"], "P18944.1") self.assertEqual(alignment.sequences[7].annotations["accession"], "O78750.1") self.assertEqual(alignment.sequences[8].annotations["accession"], "P15545.1") self.assertEqual(alignment.sequences[9].annotations["accession"], "Q06474.2") self.assertEqual(alignment.sequences[10].annotations["accession"], "A1BA41.1") self.assertEqual( alignment.sequences[0].seq, "APSSWALYFQDGASPSYLGVTHLNDYLMFYLTFIFIGVIYAICKAVIEYNYNSHPIAAKYTTHGSIVEFIWTLIPALILILVALPSFKL", ) self.assertEqual( alignment.sequences[1].seq, "VPTPYGIYFQDSATPNQEGILELHDNIMFYLFIILGLVSWMLFTIVKTYSKNPMAYKYIKHGQTIEIIWTMFPAVILLIIAFPSFIL", ) self.assertEqual( alignment.sequences[2].seq, "APSPWGIYFQDSATPQMEGLVELHDNIMYYLVVILFGVGWILLSIIRNYISTKSPISHKYLNHGTLIELIWTITPAVILILIAFPSFKL", ) self.assertEqual( alignment.sequences[3].seq, "PTPWGIFFQDSASPQMEGIEELHNNIMFYLAIILFTVTWMMITIIRNFVAKKSPIAHKYMNHGTLIELIWTITPAFILILIAFPSFKL", ) self.assertEqual( alignment.sequences[4].seq, "AEPWQLGFQDAATPIMQGIIDLHHDIFFFLILILVFVLWILVRALWHFHYKKNAIPQRIVHGTTIEILWTIFPSIILMFIAIPSFAL", ) self.assertEqual( alignment.sequences[5].seq, "MATWANLGLQDSSSPLMEQLNFFHDHTLLILTMITILVGYIMGMLSFNKFTNRFLLHGQTIEIIWTVLPAIILMFIAFPSLRL", ) self.assertEqual( alignment.sequences[6].seq, "MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLSSNTVDAQEVELIWTILPAIVLVLLALPSLQI", ) self.assertEqual( alignment.sequences[7].seq, "MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILIMIALPSLRI", ) self.assertEqual( alignment.sequences[8].seq, "MGTWAQFGLQDASSPLMEELTYFHDYALIVLTLITILVFYGLVSLLVSSNTNRFFFEGQELETIWTVIPALILILIALPSLQL", ) self.assertEqual( alignment.sequences[9].seq, "VSLWYGQNHGLMPVAASADAEKVDGIFNYMMTIATGLFLLVEGVLVYCLIRFRRRKDDQTDGPPIEGNVPLEILWTAIPTVIVFTLAVYSFEV", ) self.assertEqual( alignment.sequences[10].seq, "PVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPI", ) self.assertEqual( alignment[0], "APSSWALY---FQDGASPSYLGVTHLNDYLMFYLTFIFIGVIYAICKAVIEYNYNSHPIAAKYTTHGSI-VEFIWTLIPALILILVALPSFKL", ) self.assertEqual( alignment[1], "VPTPYGIY---FQDSATPNQEGILELHDNIMFYLFIILGLVSWMLFTIVKTY--SKNPMAYKYIKHGQT-IEIIWTMFPAVILLIIAFPSFIL", ) self.assertEqual( alignment[2], "APSPWGIY---FQDSATPQMEGLVELHDNIMYYLVVILFGVGWILLSIIRNYISTKSPISHKYLNHGTL-IELIWTITPAVILILIAFPSFKL", ) self.assertEqual( alignment[3], "-PTPWGIF---FQDSASPQMEGIEELHNNIMFYLAIILFTVTWMMITIIRNFVAKKSPIAHKYMNHGTL-IELIWTITPAFILILIAFPSFKL", ) self.assertEqual( alignment[4], "-AEPWQLG---FQDAATPIMQGIIDLHHDIFFFLILILVFVLWILVRALWHFHYKKNAIPQR-IVHGTT-IEILWTIFPSIILMFIAIPSFAL", ) self.assertEqual( alignment[5], "MATWANLG---LQDSSSPLMEQLNFFHDHTLLILTMITILVGYIMGMLSFN------KFTNRFLLHGQT-IEIIWTVLPAIILMFIAFPSLRL", ) self.assertEqual( alignment[6], "MANHSQLG---FQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLME------KLS-SNTVDAQE-VELIWTILPAIVLVLLALPSLQI", ) self.assertEqual( alignment[7], "MAYPMQLG---FQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTT------KLTHTSTMDAQE-VETIWTILPAIILIMIALPSLRI", ) self.assertEqual( alignment[8], "MGTWAQFG---LQDASSPLMEELTYFHDYALIVLTLITILVFYGLVSLLVS------SNTNRFFFEGQE-LETIWTVIPALILILIALPSLQL", ) self.assertEqual( alignment[9], "VSLWYGQNHGLMPVAASADAEKVDGIFNYMMTIATGLFLLVEGVLVYCLIRFRRRKDDQTDGPPIEGNVPLEILWTAIPTVIVFTLAVYSFEV", ) self.assertEqual( alignment[10], "-PVNGGMN---FQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPAR-FTHNTP-IEVIWTLVPVLILVAIGAFSLPI", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "hssshsls...FQDuuSP.MEtlhclHDahhhhLshIhhhVhalLshhlhpa..ptpslsp+.hhHGph.lElIWTllPAlILlhIAhPShpL", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 1, 8, 8, 48, 49, 51, 54, 57, 58, 59, 60, 66, 66, 89], [0, 1, 8, 8, 48, 49, 49, 52, 55, 56, 57, 58, 64, 64, 87], [0, 1, 8, 8, 48, 49, 51, 54, 57, 58, 59, 60, 66, 66, 89], [0, 0, 7, 7, 47, 48, 50, 53, 56, 57, 58, 59, 65, 65, 88], [0, 0, 7, 7, 47, 48, 50, 53, 56, 57, 58, 58, 64, 64, 87], [0, 1, 8, 8, 48, 48, 48, 48, 51, 52, 53, 54, 60, 60, 83], [0, 1, 8, 8, 48, 48, 48, 48, 51, 51, 52, 53, 59, 59, 82], [0, 1, 8, 8, 48, 48, 48, 48, 51, 52, 53, 54, 60, 60, 83], [0, 1, 8, 8, 48, 48, 48, 48, 51, 52, 53, 54, 60, 60, 83], [0, 1, 8, 11, 51, 52, 54, 57, 60, 61, 62, 63, 69, 70, 93], [0, 0, 7, 7, 47, 48, 50, 53, 56, 57, 58, 58, 64, 64, 87], ], ), ) ) self.assertEqual( str(alignment), """\ COX2_SCHP 0 APSSWALY---FQDGASPSYLGVTHLNDYLMFYLTFIFIGVIYAICKAVIEYNYNSHPIA COX2_CANG 0 VPTPYGIY---FQDSATPNQEGILELHDNIMFYLFIILGLVSWMLFTIVKTY--SKNPMA COX2_NEUC 0 APSPWGIY---FQDSATPQMEGLVELHDNIMYYLVVILFGVGWILLSIIRNYISTKSPIS H9D0Q0_EM 0 -PTPWGIF---FQDSASPQMEGIEELHNNIMFYLAIILFTVTWMMITIIRNFVAKKSPIA COX2_ARAT 0 -AEPWQLG---FQDAATPIMQGIIDLHHDIFFFLILILVFVLWILVRALWHFHYKKNAIP COX2_ANOG 0 MATWANLG---LQDSSSPLMEQLNFFHDHTLLILTMITILVGYIMGMLSFN------KFT COX2_CHIC 0 MANHSQLG---FQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLME------KLS COX2_SHEE 0 MAYPMQLG---FQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTT------KLT COX2_STRP 0 MGTWAQFG---LQDASSPLMEELTYFHDYALIVLTLITILVFYGLVSLLVS------SNT COX2_SYNY 0 VSLWYGQNHGLMPVAASADAEKVDGIFNYMMTIATGLFLLVEGVLVYCLIRFRRRKDDQT A1BA41_PA 0 -PVNGGMN---FQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVP COX2_SCHP 57 AKYTTHGSI-VEFIWTLIPALILILVALPSFKL 89 COX2_CANG 55 YKYIKHGQT-IEIIWTMFPAVILLIIAFPSFIL 87 COX2_NEUC 57 HKYLNHGTL-IELIWTITPAVILILIAFPSFKL 89 H9D0Q0_EM 56 HKYMNHGTL-IELIWTITPAFILILIAFPSFKL 88 COX2_ARAT 56 QR-IVHGTT-IEILWTIFPSIILMFIAIPSFAL 87 COX2_ANOG 51 NRFLLHGQT-IEIIWTVLPAIILMFIAFPSLRL 83 COX2_CHIC 51 -SNTVDAQE-VELIWTILPAIVLVLLALPSLQI 82 COX2_SHEE 51 HTSTMDAQE-VETIWTILPAIILIMIALPSLRI 83 COX2_STRP 51 NRFFFEGQE-LETIWTVIPALILILIALPSLQL 83 COX2_SYNY 60 DGPPIEGNVPLEILWTAIPTVIVFTLAVYSFEV 93 A1BA41_PA 56 AR-FTHNTP-IEVIWTLVPVLILVAIGAFSLPI 87 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID COX2_TM #=GF AC PF02790.17 #=GF DE Cytochrome C oxidase subunit II, transmembrane domain #=GF AU Sonnhammer ELL;0000-0002-9015-5588 #=GF AU Griffiths-Jones SR;0000-0001-6043-807X #=GF SE Prosite #=GF GA 22.80 18.00; #=GF TC 22.80 21.40; #=GF NC 22.70 17.90; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF WK Cytochrome_c_oxidase_subunit_II #=GF RN [1] #=GF RM 8638158 #=GF RT The whole structure of the 13-subunit oxidized cytochrome c oxidase #=GF RT at 2.8 A. #=GF RA Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S; #=GF RL Science 1996;272:1136-1144. #=GF DR INTERPRO; IPR011759; #=GF DR PROSITE; PDOC00075; #=GF DR SCOP; 1occ; fa; #=GF DC This family corresponds to chains b and o. #=GF DR TC; 3.D.4; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC The N-terminal domain of cytochrome C oxidase contains two #=GF CC transmembrane alpha-helices. #=GF SQ 11 #=GS COX2_SCHPO/11-99 AC P21534.4 #=GS COX2_CANGA/17-103 AC P43373.2 #=GS COX2_NEUCR/14-102 AC P00411.2 #=GS H9D0Q0_EMENI/15-102 AC H9D0Q0.1 #=GS COX2_ARATH/17-103 AC P93285.2 #=GS COX2_ANOGA/1-83 AC P34840.1 #=GS COX2_CHICK/1-82 AC P18944.1 #=GS COX2_SHEEP/1-83 AC O78750.1 #=GS COX2_STRPU/1-83 AC P15545.1 #=GS COX2_SYNY3/19-111 AC Q06474.2 #=GS A1BA41_PARDP/42-128 AC A1BA41.1 COX2_SCHPO/11-99 APSSWALY...FQDGASPSYLGVTHLNDYLMFYLTFIFIGVIYAICKAVIEYNYNSHPIAAKYTTHGSI.VEFIWTLIPALILILVALPSFKL COX2_CANGA/17-103 VPTPYGIY...FQDSATPNQEGILELHDNIMFYLFIILGLVSWMLFTIVKTY..SKNPMAYKYIKHGQT.IEIIWTMFPAVILLIIAFPSFIL COX2_NEUCR/14-102 APSPWGIY...FQDSATPQMEGLVELHDNIMYYLVVILFGVGWILLSIIRNYISTKSPISHKYLNHGTL.IELIWTITPAVILILIAFPSFKL H9D0Q0_EMENI/15-102 .PTPWGIF...FQDSASPQMEGIEELHNNIMFYLAIILFTVTWMMITIIRNFVAKKSPIAHKYMNHGTL.IELIWTITPAFILILIAFPSFKL COX2_ARATH/17-103 .AEPWQLG...FQDAATPIMQGIIDLHHDIFFFLILILVFVLWILVRALWHFHYKKNAIPQR.IVHGTT.IEILWTIFPSIILMFIAIPSFAL COX2_ANOGA/1-83 MATWANLG...LQDSSSPLMEQLNFFHDHTLLILTMITILVGYIMGMLSFN......KFTNRFLLHGQT.IEIIWTVLPAIILMFIAFPSLRL COX2_CHICK/1-82 MANHSQLG...FQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLME......KLS.SNTVDAQE.VELIWTILPAIVLVLLALPSLQI COX2_SHEEP/1-83 MAYPMQLG...FQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTT......KLTHTSTMDAQE.VETIWTILPAIILIMIALPSLRI COX2_STRPU/1-83 MGTWAQFG...LQDASSPLMEELTYFHDYALIVLTLITILVFYGLVSLLVS......SNTNRFFFEGQE.LETIWTVIPALILILIALPSLQL COX2_SYNY3/19-111 VSLWYGQNHGLMPVAASADAEKVDGIFNYMMTIATGLFLLVEGVLVYCLIRFRRRKDDQTDGPPIEGNVPLEILWTAIPTVIVFTLAVYSFEV A1BA41_PARDP/42-128 .PVNGGMN...FQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPAR.FTHNTP.IEVIWTLVPVLILVAIGAFSLPI #=GC seq_cons hssshsls...FQDuuSP.MEtlhclHDahhhhLshIhhhVhalLshhlhpa..ptpslsp+.hhHGph.lElIWTllPAlILlhIAhPShpL // """, ) def check_alignment_pfam7(self, alignment): """Check the alignment obtained by parsing Pfam record Alpha_E1_glycop.""" self.assertEqual(alignment.annotations["identifier"], "Alpha_E1_glycop") self.assertEqual(alignment.annotations["accession"], "PF01589.18") self.assertEqual( alignment.annotations["definition"], "Alphavirus E1 glycoprotein" ) self.assertEqual( alignment.annotations["author"], ["Bateman A;0000-0002-6982-4660"] ) self.assertEqual( alignment.annotations["source of seed"], "Pfam-B_587 (release 4.1)" ) self.assertEqual(alignment.annotations["gathering method"], "25.00 25.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "34.50 33.30;") self.assertEqual(alignment.annotations["noise cutoff"], "24.10 23.50;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Family") self.assertEqual(alignment.annotations["wikipedia"], ["Alphavirus"]) self.assertEqual(alignment.annotations["clan"], "CL0543") self.assertEqual(len(alignment.annotations["references"]), 2) self.assertEqual( alignment.annotations["references"][0]["comment"], "This paper includes cryoelectron microscopy images.", ) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "7867069") self.assertEqual( alignment.annotations["references"][0]["title"], "Nucleocapsid and glycoprotein organization in an enveloped virus.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Cheng RH, Kuhn RJ, Olson NH, Rossmann MG, Choi HK, Smith TJ, Baker TS;", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Cell 1995;80:621-630." ) self.assertEqual(alignment.annotations["references"][1]["number"], 2) self.assertEqual(alignment.annotations["references"][1]["medline"], "8995682") self.assertEqual( alignment.annotations["references"][1]["title"], "Role of glycoprotein PE2 in formation and maturation of the Sindbis virus spike.", ) self.assertEqual( alignment.annotations["references"][1]["author"], "Carleton M, Lee H, Mulvey M, Brown DT;", ) self.assertEqual( alignment.annotations["references"][1]["location"], "J Virol 1997;71:1558-1566.", ) self.assertEqual(len(alignment.annotations["database references"]), 4) self.assertEqual( alignment.annotations["database references"][0], {"reference": "INTERPRO; IPR002548;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "TC; 1.A.34;"}, ) self.assertEqual( alignment.annotations["database references"][2], {"reference": "SCOP; 1rer; fa;"}, ) self.assertEqual( alignment.annotations["database references"][3], {"reference": "SO; 0100021; polypeptide_conserved_region;"}, ) self.assertEqual( alignment.annotations["comment"], "E1 forms a heterodimer with E2 Pfam:PF00943. The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus) [2].", ) self.assertEqual(len(alignment.sequences), 2) self.assertEqual(alignment.sequences[0].id, "POLS_SFV/751-1253") self.assertEqual(alignment.sequences[1].id, "POLS_CHIKS/744-1247") self.assertEqual(alignment.sequences[0].annotations["accession"], "P03315.1") self.assertEqual(len(alignment.sequences[0].dbxrefs), 6) self.assertEqual(alignment.sequences[0].dbxrefs[0], "PDB; 2V33 A; 292-382;") self.assertEqual(alignment.sequences[0].dbxrefs[1], "PDB; 2ALA A; 1-384;") self.assertEqual(alignment.sequences[0].dbxrefs[2], "PDB; 1RER A; 1-391;") self.assertEqual(alignment.sequences[0].dbxrefs[3], "PDB; 2V33 B; 292-382;") self.assertEqual(alignment.sequences[0].dbxrefs[4], "PDB; 1RER C; 1-391;") self.assertEqual(alignment.sequences[0].dbxrefs[5], "PDB; 1RER B; 1-391;") self.assertEqual(alignment.sequences[1].annotations["accession"], "Q8JUX5.3") self.assertEqual(len(alignment.sequences[1].dbxrefs), 1) self.assertEqual(alignment.sequences[1].dbxrefs[0], "PDB; 2RSW A; 1-18;") self.assertEqual( alignment.sequences[0].seq, "PRAHAASVAETMAYLWDQNQALFWLEFAAPVACILIITYCLRNVLCCCKSLSFLVLLSLGATARAYEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR", ) self.assertEqual( alignment.sequences[1].seq, "RTAKAATYQEAAVYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSIGAHTVSAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAVSKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKITGGVGLVVAVAALILIVVLCVSFSR", ) self.assertEqual( alignment.sequences[0].letter_annotations["secondary structure"], "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEES-SS--EEEEE--TTSS-EEEEEEEEEEEEEEEEEEEEEE--EEEE----EEETSS--------STT-EEEEEES-SSSISCSCS-SSSSS-EEEEEEEEEE-TTGGGS-EEEEEEEEEEEEEEEEEEETTEEEEEEEESSSS-EEEETTEEEEE---S----S--SSEEE-SS-EEE-----GGG--TTSTTSEEBSSTT-S--EE-S--EE----SSSS---EE----HHHHHHHHS-S-GGGT-STT-EEETTTTEEES---SEEEEEESS-TTTS-EETTS--EEEEEEEEEEEBTTSTTEEEEEEEEEESS-EEEEEEESSTTEEESBSEEEE-TT-EEEEEEEESSSS-EEEEEETTEEEEEE---B----------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX", ) self.assertEqual( alignment.sequences[1].letter_annotations["secondary structure"], "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHH---STTTTS--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX", ) self.assertEqual( alignment[0], "PRAHAASVAETMAYLWDQNQALFWLEFAAPVACILIITYCLRNVLCCCKSLSFLVLLSLG-ATARAYEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR", ) self.assertEqual( alignment[1], "RTAKAATYQEAAVYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSIGAHTVSAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAVSKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKITGGVGLVVAVAALILIVVLCVSFSR", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEEEEEESXSSXXEEEEEXXTTSSXEEEEEEEEEEEEEEEEEEEEEEXXEEEEXXXXEEETSSXXXXXXXXSTTXEEEEEES-SCCHCCSCSSTTTTS-EEEEEEEEEEXTTGGGSXEEEEEEEEEEEEEEEEEEETTEEEEEEEESSSSXEEEETTEEEEEXXXSXXXXSXXSSEEEXSSXEEEXXXXXGGGXXTTSTTSEEBSSTTXSXXEEXSXXEEXXXXSSSSXXXEEXXXXHHHHHHHHSXSXGGGTXSTTXEEETTTTEEESXXXSEEEEEESSXTTTSXEETTSXXEEEEEEEEEEEBTTSTTEEEEEEEEEESSXEEEEEEESSTTEEESBSEEEEXTTXEEEEEEEESSSSXEEEEEETTEEEEEEXXXBXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX", ) self.assertEqual( alignment.column_annotations["consensus sequence"], ".pA+AAohtEshsYLWsppQsLFWLphhhPlAslllls.CLR.l.CCCKoLuFLslhSlG.tTspAYEHsTVhPNsVGhPYKshlpRPGYSPhsLpMpllpsoLEPTLsL-YITCEYKTVlPSPYVKCCGsuECpsKphPDYpCKVaTGVYPFMWGGAYCFCDuENTQLSEAaV-+S-sC+p-aASAY+AHTAShpAKlRVhYtssN.TVssYsNGDHAVTltsspFIhGPhSSAWTPFDNKIVVYKs-VaN.DaPPaGuGpPGpFGDIQSRTsESpDlYANTtLhLtRPusGhVHVPYoQsPSGFKYWLKE+GsuLpppAPFGCQItTNPVRAMNCAVGNhPlShslPDuAFTRlV-APolhDhoCpVssCTHSSDFGGVhhlpYtssKpGcCuVHShoNssTlpEAphcVcssuplplpFSTA.ASspFhVplCSspspCuApCcPPKDHIVsYsASHoslsh.DhSuTAhSWVQKIoGGlGhhshsAhLlLlVVhCluhpR", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 60, 60, 503], [0, 60, 61, 504]]) ) ) self.assertEqual( str(alignment), """\ POLS_SFV/ 0 PRAHAASVAETMAYLWDQNQALFWLEFAAPVACILIITYCLRNVLCCCKSLSFLVLLSLG 0 ..|.||...|...|||...|.||||....|.|.......|||...||||.|.||...|.| POLS_CHIK 0 RTAKAATYQEAAVYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSIG POLS_SFV/ 60 -ATARAYEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTV 60 -.|..||||.||.||.||.|||....||||||..|.|......|||||.|.||||||||| POLS_CHIK 60 AHTVSAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTV POLS_SFV/ 119 VPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVC 120 .|||||||||..||..|..|||.|||.||||||||||||||||.||||||||.|..|..| POLS_CHIK 120 IPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESC POLS_SFV/ 179 RHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFD 180 ....||||.|||||..||.||.|...|.||..|.|||||||.....||.||.|||||||| POLS_CHIK 180 KTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFD POLS_SFV/ 239 NKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYT 240 |||||||..|.|.|.||.|.|.||.||||||||.||.|.||||.|.|.||..|.|||||. POLS_CHIK 240 NKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYS POLS_SFV/ 299 QTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAP 300 |.||||||||||.|..|...|||||||.|||||||||||||.|.|...||.||||.|.|| POLS_CHIK 300 QAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAP POLS_SFV/ 359 TIIDLTCTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTL 360 ...|..|.|..||||||||||....|...|.|.|.|||..|..|..||...|........ POLS_CHIK 360 SLTDMSCEVPACTHSSDFGGVAIIKYAVSKKGKCAVHSMTNAVTIREAEIEVEGNSQLQI POLS_SFV/ 419 HFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKIS 420 .||||.||..|.|..||....|.|.|.|||||||.|.|||......|.|.||.||||||. POLS_CHIK 420 SFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKIT POLS_SFV/ 479 GGLGAFAIGAILVLVVVTCIGLRR 503 480 ||.|.....|.|.|.||.|....| 504 POLS_CHIK 480 GGVGLVVAVAALILIVVLCVSFSR 504 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID Alpha_E1_glycop #=GF AC PF01589.18 #=GF DE Alphavirus E1 glycoprotein #=GF AU Bateman A;0000-0002-6982-4660 #=GF SE Pfam-B_587 (release 4.1) #=GF GA 25.00 25.00; #=GF TC 34.50 33.30; #=GF NC 24.10 23.50; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF CL CL0543 #=GF WK Alphavirus #=GF RC This paper includes cryoelectron microscopy images. #=GF RN [1] #=GF RM 7867069 #=GF RT Nucleocapsid and glycoprotein organization in an enveloped virus. #=GF RA Cheng RH, Kuhn RJ, Olson NH, Rossmann MG, Choi HK, Smith TJ, Baker TS; #=GF RL Cell 1995;80:621-630. #=GF RN [2] #=GF RM 8995682 #=GF RT Role of glycoprotein PE2 in formation and maturation of the Sindbis #=GF RT virus spike. #=GF RA Carleton M, Lee H, Mulvey M, Brown DT; #=GF RL J Virol 1997;71:1558-1566. #=GF DR INTERPRO; IPR002548; #=GF DR TC; 1.A.34; #=GF DR SCOP; 1rer; fa; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC E1 forms a heterodimer with E2 Pfam:PF00943. The virus spikes are #=GF CC made up of 80 trimers of these heterodimers (sindbis virus) [2]. #=GF SQ 2 #=GS POLS_SFV/751-1253 AC P03315.1 #=GS POLS_SFV/751-1253 DR PDB; 2V33 A; 292-382; #=GS POLS_SFV/751-1253 DR PDB; 2ALA A; 1-384; #=GS POLS_SFV/751-1253 DR PDB; 1RER A; 1-391; #=GS POLS_SFV/751-1253 DR PDB; 2V33 B; 292-382; #=GS POLS_SFV/751-1253 DR PDB; 1RER C; 1-391; #=GS POLS_SFV/751-1253 DR PDB; 1RER B; 1-391; #=GS POLS_CHIKS/744-1247 AC Q8JUX5.3 #=GS POLS_CHIKS/744-1247 DR PDB; 2RSW A; 1-18; POLS_SFV/751-1253 PRAHAASVAETMAYLWDQNQALFWLEFAAPVACILIITYCLRNVLCCCKSLSFLVLLSLG.ATARAYEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR #=GR POLS_SFV/751-1253 SS XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX-EEEEEEES-SS--EEEEE--TTSS-EEEEEEEEEEEEEEEEEEEEEE--EEEE----EEETSS--------STT-EEEEEES-SSSISCSCS-SSSSS-EEEEEEEEEE-TTGGGS-EEEEEEEEEEEEEEEEEEETTEEEEEEEESSSS-EEEETTEEEEE---S----S--SSEEE-SS-EEE-----GGG--TTSTTSEEBSSTT-S--EE-S--EE----SSSS---EE----HHHHHHHHS-S-GGGT-STT-EEETTTTEEES---SEEEEEESS-TTTS-EETTS--EEEEEEEEEEEBTTSTTEEEEEEEEEESS-EEEEEEESSTTEEESBSEEEE-TT-EEEEEEEESSSS-EEEEEETTEEEEEE---B----------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX POLS_CHIKS/744-1247 RTAKAATYQEAAVYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSIGAHTVSAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAVSKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKITGGVGLVVAVAALILIVVLCVSFSR #=GR POLS_CHIKS/744-1247 SS XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHH---STTTTS--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #=GC SS_cons XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEEEEEESXSSXXEEEEEXXTTSSXEEEEEEEEEEEEEEEEEEEEEEXXEEEEXXXXEEETSSXXXXXXXXSTTXEEEEEES-SCCHCCSCSSTTTTS-EEEEEEEEEEXTTGGGSXEEEEEEEEEEEEEEEEEEETTEEEEEEEESSSSXEEEETTEEEEEXXXSXXXXSXXSSEEEXSSXEEEXXXXXGGGXXTTSTTSEEBSSTTXSXXEEXSXXEEXXXXSSSSXXXEEXXXXHHHHHHHHSXSXGGGTXSTTXEEETTTTEEESXXXSEEEEEESSXTTTSXEETTSXXEEEEEEEEEEEBTTSTTEEEEEEEEEESSXEEEEEEESSTTEEESBSEEEEXTTXEEEEEEEESSSSXEEEEEETTEEEEEEXXXBXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #=GC seq_cons .pA+AAohtEshsYLWsppQsLFWLphhhPlAslllls.CLR.l.CCCKoLuFLslhSlG.tTspAYEHsTVhPNsVGhPYKshlpRPGYSPhsLpMpllpsoLEPTLsL-YITCEYKTVlPSPYVKCCGsuECpsKphPDYpCKVaTGVYPFMWGGAYCFCDuENTQLSEAaV-+S-sC+p-aASAY+AHTAShpAKlRVhYtssN.TVssYsNGDHAVTltsspFIhGPhSSAWTPFDNKIVVYKs-VaN.DaPPaGuGpPGpFGDIQSRTsESpDlYANTtLhLtRPusGhVHVPYoQsPSGFKYWLKE+GsuLpppAPFGCQItTNPVRAMNCAVGNhPlShslPDuAFTRlV-APolhDhoCpVssCTHSSDFGGVhhlpYtssKpGcCuVHShoNssTlpEAphcVcssuplplpFSTA.ASspFhVplCSspspCuApCcPPKDHIVsYsASHoslsh.DhSuTAhSWVQKIoGGlGhhshsAhLlLlVVhCluhpR // """, ) def check_alignment_pfam8(self, alignment): """Check the alignment obtained by parsing Pfam record Cyclin_N.""" self.assertEqual(alignment.annotations["identifier"], "Cyclin_N") self.assertEqual(alignment.annotations["accession"], "PF00134.25") self.assertEqual( alignment.annotations["definition"], "Cyclin, N-terminal domain" ) self.assertEqual(alignment.annotations["previous identifier"], "cyclin;") self.assertEqual( alignment.annotations["author"], [ "Bateman A;0000-0002-6982-4660", "Sonnhammer ELL;0000-0002-9015-5588", "Griffiths-Jones SR;0000-0001-6043-807X", ], ) self.assertEqual(alignment.annotations["source of seed"], "Prosite") self.assertEqual(alignment.annotations["gathering method"], "20.50 20.50;") self.assertEqual(alignment.annotations["trusted cutoff"], "20.50 20.50;") self.assertEqual(alignment.annotations["noise cutoff"], "20.40 20.40;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Domain") self.assertEqual(alignment.annotations["wikipedia"], ["Cyclin"]) self.assertEqual(alignment.annotations["clan"], "CL0065") self.assertEqual( alignment.annotations["references"][0]["comment"], "The cyclins include an internal duplication, which is related to that found in TFIIB and the RB protein.", ) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "8152925") self.assertEqual( alignment.annotations["references"][0]["title"], "Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Gibson TJ, Thompson JD, Blocker A, Kouzarides T;", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Nucleic Acids Res 1994;22:946-952.", ) self.assertEqual(alignment.annotations["references"][1]["number"], 2) self.assertEqual(alignment.annotations["references"][1]["medline"], "8591034") self.assertEqual( alignment.annotations["references"][1]["title"], "The crystal structure of cyclin A", ) self.assertEqual( alignment.annotations["references"][1]["author"], "Brown NR, Noble MEM, Endicott JA, Garman EF, Wakatsuki S, Mitchell E, Rasmussen B, Hunt T, Johnson LN;", ) self.assertEqual( alignment.annotations["references"][1]["location"], "Structure. 1995;3:1235-1247.", ) self.assertEqual( alignment.annotations["references"][2]["comment"], "Complex of cyclin and cyclin dependent kinase.", ) self.assertEqual(alignment.annotations["references"][2]["number"], 3) self.assertEqual(alignment.annotations["references"][2]["medline"], "8756328") self.assertEqual( alignment.annotations["references"][2]["title"], "Structural basis of cyclin-dependant kinase activation by phosphorylation.", ) self.assertEqual( alignment.annotations["references"][2]["author"], "Russo AA, Jeffrey PD, Pavletich NP;", ) self.assertEqual( alignment.annotations["references"][2]["location"], "Nat Struct Biol. 1996;3:696-700.", ) self.assertEqual(alignment.annotations["references"][3]["number"], 4) self.assertEqual(alignment.annotations["references"][3]["medline"], "2001396") self.assertEqual( alignment.annotations["references"][3]["title"], "Isolation and characterization of a human cDNA encoding uracil-DNA glycosylase.", ) self.assertEqual( alignment.annotations["references"][3]["author"], "Muller SJ, Caradonna S;" ) self.assertEqual( alignment.annotations["references"][3]["location"], "Biochim Biophys Acta 1991;1088:197-207.", ) self.assertEqual(len(alignment.annotations["database references"]), 5) self.assertEqual( alignment.annotations["database references"][0], {"reference": "INTERPRO; IPR006671;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "PROSITE; PDOC00264;"}, ) self.assertEqual( alignment.annotations["database references"][2], {"reference": "SCOP; 1vin; fa;"}, ) self.assertEqual( alignment.annotations["database references"][3], {"reference": "HOMSTRAD; cyclin;"}, ) self.assertEqual( alignment.annotations["database references"][4], {"reference": "SO; 0000417; polypeptide_domain;"}, ) self.assertEqual( alignment.annotations["comment"], "Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.", ) self.assertEqual(len(alignment.sequences), 95) self.assertEqual(alignment.sequences[0].id, "CCNB3_CAEEL/115-241") self.assertEqual(alignment.sequences[1].id, "T1FNQ9_HELRO/256-381") self.assertEqual(alignment.sequences[2].id, "CCNB3_DROME/308-433") self.assertEqual(alignment.sequences[3].id, "CCNB3_CHICK/149-274") self.assertEqual(alignment.sequences[4].id, "CCB31_ARATH/146-272") self.assertEqual(alignment.sequences[5].id, "CCNB1_SOYBN/197-322") self.assertEqual(alignment.sequences[6].id, "CCB11_ARATH/168-293") self.assertEqual(alignment.sequences[7].id, "CCB12_ARATH/185-310") self.assertEqual(alignment.sequences[8].id, "M1A5P4_SOLTU/185-310") self.assertEqual(alignment.sequences[9].id, "I1M770_SOYBN/186-311") self.assertEqual(alignment.sequences[10].id, "CCB14_ARATH/133-258") self.assertEqual(alignment.sequences[11].id, "B8A2G9_MAIZE/228-354") self.assertEqual(alignment.sequences[12].id, "B4FZZ7_MAIZE/193-318") self.assertEqual(alignment.sequences[13].id, "K7V0X7_MAIZE/191-316") self.assertEqual(alignment.sequences[14].id, "CCB21_ORYSJ/157-283") self.assertEqual(alignment.sequences[15].id, "CCB21_ARATH/174-300") self.assertEqual(alignment.sequences[16].id, "Q9XGI1_SOLLC/180-306") self.assertEqual(alignment.sequences[17].id, "C4J9B6_MAIZE/173-299") self.assertEqual(alignment.sequences[18].id, "CCB24_ARATH/180-307") self.assertEqual(alignment.sequences[19].id, "CCNB_DICDI/188-314") self.assertEqual(alignment.sequences[20].id, "O45926_CAEEL/34-159") self.assertEqual(alignment.sequences[21].id, "CCNB1_CAEEL/81-206") self.assertEqual(alignment.sequences[22].id, "P92162_BOMMO/260-387") self.assertEqual(alignment.sequences[23].id, "CCNB_DROME/260-387") self.assertEqual(alignment.sequences[24].id, "F6QF79_XENTR/139-264") self.assertEqual(alignment.sequences[25].id, "CCNB1_MOUSE/170-295") self.assertEqual(alignment.sequences[26].id, "Q28HA1_XENTR/132-257") self.assertEqual(alignment.sequences[27].id, "CCNB2_HUMAN/137-262") self.assertEqual(alignment.sequences[28].id, "CCNB2_CHICK/141-266") self.assertEqual(alignment.sequences[29].id, "A0BXX7_PARTE/85-212") self.assertEqual(alignment.sequences[30].id, "Q6BFS2_PARTE/82-210") self.assertEqual(alignment.sequences[31].id, "CG21_CANAL/208-334") self.assertEqual(alignment.sequences[32].id, "CGS5_YEAST/165-294") self.assertEqual(alignment.sequences[33].id, "CGS6_YEAST/123-252") self.assertEqual(alignment.sequences[34].id, "CG21_YEAST/212-337") self.assertEqual(alignment.sequences[35].id, "CG22_YEAST/232-357") self.assertEqual(alignment.sequences[36].id, "CG24_CANAL/234-360") self.assertEqual(alignment.sequences[37].id, "CG23_YEAST/171-297") self.assertEqual(alignment.sequences[38].id, "CG24_YEAST/210-336") self.assertEqual(alignment.sequences[39].id, "CG22_SCHPO/139-265") self.assertEqual(alignment.sequences[40].id, "M7PCR8_PNEMU/176-302") self.assertEqual(alignment.sequences[41].id, "CG21_EMENI/211-337") self.assertEqual(alignment.sequences[42].id, "CG23_SCHPO/206-332") self.assertEqual(alignment.sequences[43].id, "CG21_SCHPO/166-292") self.assertEqual(alignment.sequences[44].id, "REM1_SCHPO/145-271") self.assertEqual(alignment.sequences[45].id, "CCNF_MOUSE/282-406") self.assertEqual(alignment.sequences[46].id, "I1K835_SOYBN/85-214") self.assertEqual(alignment.sequences[47].id, "J3KY10_ORYBR/200-327") self.assertEqual(alignment.sequences[48].id, "M4E4A3_BRARP/154-281") self.assertEqual(alignment.sequences[49].id, "CCA22_ARATH/175-302") self.assertEqual(alignment.sequences[50].id, "Q39878_SOYBN/207-334") self.assertEqual(alignment.sequences[51].id, "T1EGC7_HELRO/166-291") self.assertEqual(alignment.sequences[52].id, "CCNA1_CAEEL/215-341") self.assertEqual(alignment.sequences[53].id, "CCNA_DROME/206-332") self.assertEqual(alignment.sequences[54].id, "W4XJF2_STRPU/207-333") self.assertEqual(alignment.sequences[55].id, "CCNA2_MOUSE/171-297") self.assertEqual(len(alignment.sequences[55].dbxrefs), 8) self.assertEqual(alignment.sequences[55].dbxrefs[0], "PDB; 4I3Z D; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[1], "PDB; 4II5 D; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[2], "PDB; 4I3Z B; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[3], "PDB; 4II5 B; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[4], "PDB; 3QHW B; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[5], "PDB; 3QHW D; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[6], "PDB; 3QHR D; 181-307;") self.assertEqual(alignment.sequences[55].dbxrefs[7], "PDB; 3QHR B; 181-307;") self.assertEqual( alignment.sequences[55].letter_annotations["secondary structure"], "HHHHHHHHHHHHT---TTGGGG-SS--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHCC----CCCHHHHHHHHHHHHHHHH-SS---HHHHHHHTTTSS-HHHHHHHHHHHHHHHTT---", ) self.assertEqual(alignment.sequences[56].id, "E9QJ66_DANRE/140-266") self.assertEqual(alignment.sequences[57].id, "CCNA1_HUMAN/214-340") self.assertEqual(alignment.sequences[58].id, "CG12_YEAST/43-195") self.assertEqual(alignment.sequences[59].id, "PUC1_SCHPO/99-227") self.assertEqual(alignment.sequences[60].id, "CG13_CANAL/44-172") self.assertEqual(alignment.sequences[61].id, "CG11_CANAL/44-172") self.assertEqual(alignment.sequences[62].id, "CGH2_SHV21/22-148") self.assertEqual(len(alignment.sequences[62].dbxrefs), 6) self.assertEqual(alignment.sequences[62].dbxrefs[0], "PDB; 1JOW A; 22-148;") self.assertEqual(alignment.sequences[62].dbxrefs[1], "PDB; 1BU2 A; 22-148;") self.assertEqual(alignment.sequences[62].dbxrefs[2], "PDB; 2EUF A; 22-148;") self.assertEqual(alignment.sequences[62].dbxrefs[3], "PDB; 4TTH A; 22-148;") self.assertEqual(alignment.sequences[62].dbxrefs[4], "PDB; 1XO2 A; 22-148;") self.assertEqual(alignment.sequences[62].dbxrefs[5], "PDB; 2F2C A; 22-148;") self.assertEqual( alignment.sequences[62].letter_annotations["secondary structure"], "HHHHHHHHHHTTS---SSTTTT-SSS-HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---TTTHHHHHHHHHHHHHHHHSSS---HHHHHHTTTTSS-HHHHHHHHHHHHHHTTT---", ) self.assertEqual(alignment.sequences[63].id, "VCYCL_HHV8P/21-147") self.assertEqual(alignment.sequences[64].id, "CCND_CAEEL/72-201") self.assertEqual(alignment.sequences[65].id, "Q7KUZ5_DROME/153-280") self.assertEqual(alignment.sequences[66].id, "CCND1_RAT/26-153") self.assertEqual(alignment.sequences[67].id, "CCND2_MOUSE/24-151") self.assertEqual(alignment.sequences[68].id, "CCND3_HUMAN/26-153") self.assertEqual(len(alignment.sequences[68].dbxrefs), 2) self.assertEqual(alignment.sequences[68].dbxrefs[0], "PDB; 3G33 D; 26-153;") self.assertEqual(alignment.sequences[68].dbxrefs[1], "PDB; 3G33 B; 26-153;") self.assertEqual( alignment.sequences[68].letter_annotations["secondary structure"], "HHHHHHHHHGGGGS-SS--TTTSTTT--HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHH----GGGHHHHHHHHHHHHHHHH-SS---TTHHHHHTTTSS-HHHHHHHHHHHHHHTTT---", ) self.assertEqual(alignment.sequences[69].id, "Q9VZP3_DROME/42-165") self.assertEqual(alignment.sequences[70].id, "SSN8_YEAST/45-176") self.assertEqual(alignment.sequences[71].id, "CCC11_ORYSJ/4-144") self.assertEqual(alignment.sequences[72].id, "CCNT_DROME/42-176") self.assertEqual(alignment.sequences[73].id, "CCT12_ARATH/28-169") self.assertEqual(alignment.sequences[74].id, "Q9VE72_DROME/6-144") self.assertEqual(alignment.sequences[75].id, "PCL1_YEAST/19-152") self.assertEqual(alignment.sequences[76].id, "PCL2_YEAST/18-146") self.assertEqual(alignment.sequences[77].id, "PCL9_YEAST/19-146") self.assertEqual(alignment.sequences[78].id, "CCU41_ARATH/23-148") self.assertEqual(alignment.sequences[79].id, "Q9VKF0_DROME/205-327") self.assertEqual(alignment.sequences[80].id, "CCD11_ARATH/50-182") self.assertEqual(alignment.sequences[81].id, "CCD21_ARATH/65-197") self.assertEqual(alignment.sequences[82].id, "CCD41_ARATH/45-178") self.assertEqual(alignment.sequences[83].id, "Q9SMD4_SOLLC/51-182") self.assertEqual(alignment.sequences[84].id, "Q9S7H9_SOLLC/61-190") self.assertEqual(alignment.sequences[85].id, "CCD33_ARATH/59-186") self.assertEqual(alignment.sequences[86].id, "CCD61_ARATH/26-154") self.assertEqual(alignment.sequences[87].id, "CCNE_DROME/330-459") self.assertEqual(alignment.sequences[88].id, "CCNE2_MOUSE/112-239") self.assertEqual(alignment.sequences[89].id, "CCNE1_CHICK/112-239") self.assertEqual(alignment.sequences[90].id, "CCNE1_MOUSE/113-240") self.assertEqual(alignment.sequences[91].id, "A0A0R4IZF8_DANRE/117-244") self.assertEqual(alignment.sequences[92].id, "F6QUN0_XENTR/114-241") self.assertEqual(alignment.sequences[93].id, "W4XEA0_STRPU/126-253") self.assertEqual(alignment.sequences[94].id, "CCNE_CAEEL/232-360") self.assertEqual(alignment.sequences[0].annotations["accession"], "Q10654.3") self.assertEqual(alignment.sequences[1].annotations["accession"], "T1FNQ9.1") self.assertEqual(alignment.sequences[2].annotations["accession"], "Q9I7I0.1") self.assertEqual(alignment.sequences[3].annotations["accession"], "P39963.1") self.assertEqual(alignment.sequences[4].annotations["accession"], "Q9SA32.2") self.assertEqual(alignment.sequences[5].annotations["accession"], "P25011.1") self.assertEqual(alignment.sequences[6].annotations["accession"], "P30183.2") self.assertEqual(alignment.sequences[7].annotations["accession"], "Q39067.2") self.assertEqual(alignment.sequences[8].annotations["accession"], "M1A5P4.1") self.assertEqual(alignment.sequences[9].annotations["accession"], "I1M770.1") self.assertEqual(alignment.sequences[10].annotations["accession"], "O48790.1") self.assertEqual(alignment.sequences[11].annotations["accession"], "B8A2G9.1") self.assertEqual(alignment.sequences[12].annotations["accession"], "B4FZZ7.1") self.assertEqual(alignment.sequences[13].annotations["accession"], "K7V0X7.1") self.assertEqual(alignment.sequences[14].annotations["accession"], "Q7XSJ6.2") self.assertEqual(alignment.sequences[15].annotations["accession"], "Q39068.2") self.assertEqual(alignment.sequences[16].annotations["accession"], "Q9XGI1.1") self.assertEqual(alignment.sequences[17].annotations["accession"], "C4J9B6.1") self.assertEqual(alignment.sequences[18].annotations["accession"], "Q9SFW6.2") self.assertEqual(alignment.sequences[19].annotations["accession"], "P42524.1") self.assertEqual(alignment.sequences[20].annotations["accession"], "O45926.2") self.assertEqual(alignment.sequences[21].annotations["accession"], "Q10653.1") self.assertEqual(alignment.sequences[22].annotations["accession"], "P92162.1") self.assertEqual(alignment.sequences[23].annotations["accession"], "P20439.2") self.assertEqual(alignment.sequences[24].annotations["accession"], "F6QF79.3") self.assertEqual(alignment.sequences[25].annotations["accession"], "P24860.3") self.assertEqual(alignment.sequences[26].annotations["accession"], "Q28HA1.1") self.assertEqual(alignment.sequences[27].annotations["accession"], "O95067.1") self.assertEqual(alignment.sequences[28].annotations["accession"], "P29332.1") self.assertEqual(alignment.sequences[29].annotations["accession"], "A0BXX7.1") self.assertEqual(alignment.sequences[30].annotations["accession"], "Q6BFS2.1") self.assertEqual(alignment.sequences[31].annotations["accession"], "Q5ALY0.1") self.assertEqual(alignment.sequences[32].annotations["accession"], "P30283.1") self.assertEqual(alignment.sequences[33].annotations["accession"], "P32943.2") self.assertEqual(alignment.sequences[34].annotations["accession"], "P24868.1") self.assertEqual(alignment.sequences[35].annotations["accession"], "P24869.1") self.assertEqual(alignment.sequences[36].annotations["accession"], "Q5A0A9.1") self.assertEqual(alignment.sequences[37].annotations["accession"], "P24870.3") self.assertEqual(alignment.sequences[38].annotations["accession"], "P24871.2") self.assertEqual(alignment.sequences[39].annotations["accession"], "P36630.2") self.assertEqual(alignment.sequences[40].annotations["accession"], "M7PCR8.1") self.assertEqual(alignment.sequences[41].annotations["accession"], "P30284.1") self.assertEqual(alignment.sequences[42].annotations["accession"], "P10815.1") self.assertEqual(alignment.sequences[43].annotations["accession"], "P24865.2") self.assertEqual(alignment.sequences[44].annotations["accession"], "O14332.1") self.assertEqual(alignment.sequences[45].annotations["accession"], "P51944.2") self.assertEqual(alignment.sequences[46].annotations["accession"], "I1K835.1") self.assertEqual(alignment.sequences[47].annotations["accession"], "J3KY10.1") self.assertEqual(alignment.sequences[48].annotations["accession"], "M4E4A3.1") self.assertEqual(alignment.sequences[49].annotations["accession"], "Q147G5.1") self.assertEqual(alignment.sequences[50].annotations["accession"], "Q39878.1") self.assertEqual(alignment.sequences[51].annotations["accession"], "T1EGC7.1") self.assertEqual(alignment.sequences[52].annotations["accession"], "P34638.2") self.assertEqual(alignment.sequences[53].annotations["accession"], "P14785.3") self.assertEqual(alignment.sequences[54].annotations["accession"], "W4XJF2.1") self.assertEqual(alignment.sequences[55].annotations["accession"], "P51943.2") self.assertEqual(alignment.sequences[56].annotations["accession"], "E9QJ66.1") self.assertEqual(alignment.sequences[57].annotations["accession"], "P78396.1") self.assertEqual(alignment.sequences[58].annotations["accession"], "P20438.2") self.assertEqual(alignment.sequences[59].annotations["accession"], "P25009.1") self.assertEqual(alignment.sequences[60].annotations["accession"], "Q5A1N6.1") self.assertEqual(alignment.sequences[61].annotations["accession"], "Q59YH3.2") self.assertEqual(alignment.sequences[62].annotations["accession"], "Q01043.1") self.assertEqual(alignment.sequences[63].annotations["accession"], "Q77Q36.1") self.assertEqual(alignment.sequences[64].annotations["accession"], "Q9U2M5.1") self.assertEqual(alignment.sequences[65].annotations["accession"], "Q7KUZ5.1") self.assertEqual(alignment.sequences[66].annotations["accession"], "P39948.1") self.assertEqual(alignment.sequences[67].annotations["accession"], "P30280.1") self.assertEqual(alignment.sequences[68].annotations["accession"], "P30281.2") self.assertEqual(alignment.sequences[69].annotations["accession"], "Q9VZP3.1") self.assertEqual(alignment.sequences[70].annotations["accession"], "P47821.1") self.assertEqual(alignment.sequences[71].annotations["accession"], "P93411.1") self.assertEqual(alignment.sequences[72].annotations["accession"], "O96433.2") self.assertEqual(alignment.sequences[73].annotations["accession"], "Q56YF8.2") self.assertEqual(alignment.sequences[74].annotations["accession"], "Q9VE72.1") self.assertEqual(alignment.sequences[75].annotations["accession"], "P24867.1") self.assertEqual(alignment.sequences[76].annotations["accession"], "P25693.2") self.assertEqual(alignment.sequences[77].annotations["accession"], "Q12477.1") self.assertEqual(alignment.sequences[78].annotations["accession"], "O80513.1") self.assertEqual(alignment.sequences[79].annotations["accession"], "Q9VKF0.1") self.assertEqual(alignment.sequences[80].annotations["accession"], "P42751.3") self.assertEqual(alignment.sequences[81].annotations["accession"], "P42752.3") self.assertEqual(alignment.sequences[82].annotations["accession"], "Q8LGA1.2") self.assertEqual(alignment.sequences[83].annotations["accession"], "Q9SMD4.1") self.assertEqual(alignment.sequences[84].annotations["accession"], "Q9S7H9.1") self.assertEqual(alignment.sequences[85].annotations["accession"], "Q9SN11.1") self.assertEqual(alignment.sequences[86].annotations["accession"], "Q9ZR04.1") self.assertEqual(alignment.sequences[87].annotations["accession"], "P54733.2") self.assertEqual(alignment.sequences[88].annotations["accession"], "Q9Z238.1") self.assertEqual(alignment.sequences[89].annotations["accession"], "P49707.1") self.assertEqual(alignment.sequences[90].annotations["accession"], "Q61457.2") self.assertEqual( alignment.sequences[91].annotations["accession"], "A0A0R4IZF8.1" ) self.assertEqual(alignment.sequences[92].annotations["accession"], "F6QUN0.2") self.assertEqual(alignment.sequences[93].annotations["accession"], "W4XEA0.1") self.assertEqual(alignment.sequences[94].annotations["accession"], "O01501.2") self.assertEqual( alignment.sequences[0].seq, "GIFDYYRHREVHFRVRKYLHKHPEVDVKTRAILIDWMVEIQETFELNHETLYNAVKLTDMYLCKTKNVDKNTIQKLACVAIFIAAKYDERSPPLVDDLIYLSGDRFSRDELLAMERELFATVGYDLG", ) self.assertEqual( alignment.sequences[1].seq, "DIFDYYRDREVKFRIPDYMFQQTDLTPSMRAILVDWLVEVQQSFELNHETLYMAVKLIDIFSSKVTIKRNKLQLIGAVALNLACKFEERCPPMLDDFVYVCDDAYPRQEFLKMEELVFQAVGFDIG", ) self.assertEqual( alignment.sequences[2].seq, "DIFNYLKVREAEFPIADYMPRQIHLTTWMRTLLVDWMVEVQETFELNHETLYLAVKIVDLYLCREVINKEKLQLLGAAAFFIACKYDERQPPLIEDFLYICDGAYNHDELVRMERETLRVIKYDLG", ) self.assertEqual( alignment.sequences[3].seq, "EIFDYMREREEKFLLPDYMEKQSDISRDMRAILVDWMVEVQENFELNHETLYLAVKLVDHYLVEVVSMRDKLQLIGSTAVLIASKFEERCPPCVDDFLYICDDAYKREELIAMETSILRTLNFDIN", ) self.assertEqual( alignment.sequences[4].seq, "DIYQFYWTAEALNPALGHYLSAHAEVSPVTRGILINWLIEVHFKFDLMHETLYLTMDLLDRYLSQVPIHKNEMQLIGLTALLLASKYEDYWHPRIKDLISISAESYTREQILGMERSMLKQLKFRLN", ) self.assertEqual( alignment.sequences[5].seq, "DIYKFYKLVENESRPHDYIGSQPEINERMRAILVDWLIDVHTKFELSLETLYLTINIIDRFLAVKTVPRRELQLVGISAMLMASKYEEIWPPEVNDFVCLSDRAYTHEHILTMEKTILNKLEWTLT", ) self.assertEqual( alignment.sequences[6].seq, "DIYSFYKSVESEWRPRDYMASQPDINEKMRLILVEWLIDVHVRFELNPETFYLTVNILDRFLSVKPVPRKELQLVGLSALLMSAKYEEIWPPQVEDLVDIADHAYSHKQILVMEKTILSTLEWYLT", ) self.assertEqual( alignment.sequences[7].seq, "DMYSFYKEVEKESQPKMYMHIQTEMNEKMRAILIDWLLEVHIKFELNLETLYLTVNIIDRFLSVKAVPKRELQLVGISALLIASKYEEIWPPQVNDLVYVTDNAYSSRQILVMEKAILGNLEWYLT", ) self.assertEqual( alignment.sequences[8].seq, "DIYKFYKLTEDENRPCDYMDSQPEINDRVRAILVDWLIEAHKRFELRPESLYLTVNIMDRFLSEETVPRRELQLLCISSMLIACKYEEIWAPEVNDFLTITDNAYVRDQILLMEKVILGKLEWYLT", ) self.assertEqual( alignment.sequences[9].seq, "DIYKFYKETEEDGCVHDYMGSQPDINAKMRSILVDWLIEVHRKFELMPETLYLTLNIVDRFLSVKAVPRRELQLVGISSMLIASKYEEIWAPEVNDFVCISDNAYVSEQVLMMEKTILRKLEWYLT", ) self.assertEqual( alignment.sequences[10].seq, "DIFKFYRTVEEEGGIKDYIGSQPEINEKMRSILIDWLVDVHRKFELMPETLYLTINLVDRFLSLTMVHRRELQLLGLGAMLIACKYEEIWAPEVNDFVCISDNAYNRKQVLAMEKSILGQVEWYIT", ) self.assertEqual( alignment.sequences[11].seq, "DIYRFYKSTEGTCLPLSSYMSSQAEISERMRAILIDWIIEVQYRLTLMPETLYLTVYIIDQYLSMESVPRKELQLVGISAMLIASKYEEIWAPLVKDLMCLCDNAFTRDQILTKEKAILDMLHWNLT", ) self.assertEqual( alignment.sequences[12].seq, "DIYTFYKIAQHDRRPCDYIDTQVEINPKMRAILAGWIIEVHHKFELMPETLYLTMYIIDQYLSLQPVLRRELQLVGVSAMLIACKYEEIWAPEVNDFILISDSAYSREQILSMEKGILNSLEWNLT", ) self.assertEqual( alignment.sequences[13].seq, "DIYTFYKTAQHESRPIDYMGNQPELSPRMRSILADWLIESHRRFQLMPETLYLTIYIVDRYLSLQPTPRRELQLVGVAALLIACKYEEIWAPEVNDLIHIADGAFNRSQILAAEKAILNSMEWNLT", ) self.assertEqual( alignment.sequences[14].seq, "ELYKFYRENEEMSCVQPDYMSSQGDINEKMRAILIDWLIEVHHKFELMDETLFLTVNIVDRFLEKQVVPRKKLQLVGVTAMLLACKYEEVAVPVVEDLVLISDRAYTKGQILEMEKLILNTLQFNMS", ) self.assertEqual( alignment.sequences[15].seq, "DLYAFYRTMERFSCVPVDYMMQQIDLNEKMRAILIDWLIEVHDKFDLINETLFLTVNLIDRFLSKQNVMRKKLQLVGLVALLLACKYEEVSVPVVEDLVLISDKAYTRNDVLEMEKTMLSTLQFNIS", ) self.assertEqual( alignment.sequences[16].seq, "DLFANYRTMEVNSCASPYYMAQQADINERMRSILIDWLIEVHHKFELREETLFLTVNLIDRFLEKQGIVRKKLQLVGLVAMLLACKYEEVCAPLVEDLVLISDKAYTRKEVLEMESMMLNTLQFNMS", ) self.assertEqual( alignment.sequences[17].seq, "EIYRFYRKTEGASCVPTNYMSSQTDINEKMRGILIDWLIEVHYKLELLEETLFLTVNIIDRFLARENVVRKKLQLAGVTAMLLACKYEEVSVPVVEDLILICDRAYTRADILEMERRIVNTLNFNMS", ) self.assertEqual( alignment.sequences[18].seq, "DIYCFYKKNECRSCVPPNYMENQHDINERMRGILFDWLIEVHYKFELMEETLYLTINLIDRFLAVHQHIARKKLQLVGVTAMLLACKYEEVSVPVVDDLILISDKAYTRTEILDMEKLMANTLQFNFC", ) self.assertEqual( alignment.sequences[19].seq, "EIFAYYREKEQIDKIDKDYIKNQYHINERMRAILVDWMMAVHVRFKLLSETFFLSVNIVDRYLAKVMIPVTKLQLVGITAILLACKYEEIYSPQIKDFVHTSDDACTHAEVIDMERQILSTLQFHMS", ) self.assertEqual( alignment.sequences[20].seq, "DIYNYLVHHEKKYVLDDSFINGGNVNSKMRRILVDWLIQVHLRFHLTPETLHLTIFVLDRIIVKNIVSKAEFQLLGVAALFVASKFEDIYLPDILEYEMITDNTFSKKQIMAMEQTILNALNFDLS", ) self.assertEqual( alignment.sequences[21].seq, "DIYKYLVHHEKKYLLEECFMEGGEPTPKMRRILVDWLVQVHVRFHLTPETLHLTVFILDRMLQKKVTSKADLQLLGISAMFVASKFEEVYLPDIHDYEFITENTYSKKQILAMEQTILNSLNFDLS", ) self.assertEqual( alignment.sequences[22].seq, "DIYKYLTELEEKYSIEPDHLKKQTVITGKMRATLIDWLVEVQRQFSLVLETFHLTVGIIDRYLQVVPNVQRNQLQLVGVTAMFIASKYEEIYAPDVGDFVYVTDNAYTKSDVFRCERDIMCKLGFCLA", ) self.assertEqual( alignment.sequences[23].seq, "DIYDYLYQVELEQPIHKDHLAGQKEVSHKMRAVLIDWINEVHLQFHLAAETFQLAVAIIDRYLQVVKDTKRTYLQLVGVTALFIATKYEELFPPAIGDFVFITDDTYTARQIRQMELQIFKAIDCNLS", ) self.assertEqual( alignment.sequences[24].seq, "DIYCYLRSLENAQAVRQNYLHGQEVTGNMRAILIDWLVQVQMKFRLLQETMFMTVGIIDRFLQDHPVPKNQLQLVGVTAMFLAAKYEEMYPPEIGDFTFVTDHTYTKAQIRDMEMKVLRVLKFAIG", ) self.assertEqual( alignment.sequences[25].seq, "DIYAYLRQLEEEQSVRPKYLQGREVTGNMRAILIDWLIQVQMKFRLLQETMYMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTNNTYTKHQIRQMEMKILRVLNFSLG", ) self.assertEqual( alignment.sequences[26].seq, "DIYNYLKQLEVQQSVRPCYLEGKEINERMRAILVDWIVQVHSRFQLLQETLYMGIAIMDRFLQVQPVSRSKLQLVGVTSLLVASKYEEMYTPEVADFVYITDNAYTASQIREMEMIILRVLNFDLG", ) self.assertEqual( alignment.sequences[27].seq, "DIYQYLRQLEVLQSINPHFLDGRDINGRMRAILVDWLVQVHSKFRLLQETLYMCVGIMDRFLQVQPVSRKKLQLVGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREMETLILKELKFELG", ) self.assertEqual( alignment.sequences[28].seq, "DIYLYLRQLELQQSVRPHYLDGKTINGRMRAILVDWLVQVHSRFQLLQETLYMCVAVMDRFLQSHPVPRKRLQLVGVTALLLASKYEEMYSPDIADFVYITDNAYNSAEVREMEITILKELNFDLG", ) self.assertEqual( alignment.sequences[29].seq, "EILQHLLIEENKYTINQYMTPEQQPDINIKMRAILVDWLIDVHAKFKLKDETLYITISLIDRYLALAQVTRMRLQLVGVAALFIACKYEEIYPPALKDFVYITDNAYVKSDVLEMEGLMLQALNFNIC", ) self.assertEqual( alignment.sequences[30].seq, "EIYTYLLTQEEKYLVSNNYMNEQQQPDLNARMRAILLDWLIDVHLKFKLRDETLYVTTYLIDRFLNFKTTTRQQLQLVGVASLFIACKYEEIYPPDLKDFVYITDNAYTKQDVLEMEGQILQTLDFSIT", ) self.assertEqual( alignment.sequences[31].seq, "EIFSYYYELETRMLPDPQYLFKQTLLKPRMRSILVDWLVEMHLKFKLLPESLFLAVNVMDRFMSVEVVQIDKLQLLATAALFTAAKYEEVFSPSVKNYAYFTDGSYTPEEVVQAEKYMLTILNFDLN", ) self.assertEqual( alignment.sequences[32].seq, "EIFAFLYRRELETLPSHNYLLDKTSKYYLRPSMRTILVDWLVEVHEKFQCYPETLFLSINLMDRFLAKNKVTMNKLQLLAVTSLFIAAKFEEVNLPKLAEYAYITDGAASKNDIKNAEMFMLTSLEFNIG", ) self.assertEqual( alignment.sequences[33].seq, "SIFSHLYEKEIQMLPTHNYLMDTQSPYHLKSSMRALLIDWLVEVHEKFHCLPETLFLAINLLDRFLSQNVVKLNKLQLLCITCLFIACKFEEVKLPKITNFAYVTDGAATVEGIRKAELFVLSSLGYNIS", ) self.assertEqual( alignment.sequences[34].seq, "DIFDYLHHLEIITLPNKANLYKHKNIKQNRDILVNWIIKIHNKFGLLPETLYLAINIMDRFLCEEVVQLNRLQLVGTSCLFIASKYEEIYSPSIKHFAYETDGACSVEDIKEGERFILEKLDFQIS", ) self.assertEqual( alignment.sequences[35].seq, "DIFEYLHQLEVITLPKKEDLYQHRNIHQNRDILVNWLVKIHNKFGLLPETLYLAINIMDRFLGKELVQLDKLQLVGTSCLFIASKYEEVYSPSIKHFASETDGACTEDEIKEGEKFILKTLKFNLN", ) self.assertEqual( alignment.sequences[36].seq, "EIFNYLHELENKFTPDPNYMDFQDDLKWEMRAVLIDWVVQVHARFNLFSETLYLTVNYIDRFLSKRRVSLSRFQLVGAVALFIAAKYEEINCPTVQEIAYMADNAYSIDEFLKAERFMIDVLEFDLG", ) self.assertEqual( alignment.sequences[37].seq, "EIFEYMRKLEDLYKPNPYYMDKQPELRWSFRSTLIDWIVQVHEKFQLLPETLYLCINIIDRYLCKEVVPVNKFQLVGAASLFIAAKYEEINCPTIKDFVYMSENCYSRNDLLDAERTILNGLEFELG", ) self.assertEqual( alignment.sequences[38].seq, "DIFYYLRELEVKYRPNPYYMQNQVELTWPFRRTMIDWLVQLHFRFQLLPETLYLTINIVDRFLSKKTVTLNRFQLVGVSALFIAAKFEEINCPTLDDLVYMLENTYTRDDIIRAEQYMIDTLEFEIG", ) self.assertEqual( alignment.sequences[39].seq, "EIFEYIRKLDLKCLPNPKYMDQQKELTWKMREILNEWLVEIHSNFCLMPETLYLAVNIIDRFLSRRSCSLSKFQLTGITALLIASKYEEVMCPSIQNFVYMTDGAFTVEDVCVAERYMLNVLNFDLS", ) self.assertEqual( alignment.sequences[40].seq, "EIMSYMRELEVLTLPLPDYMDRQKELQWKMRGILVDWLIEVHAKFRLLPETLFLSVNIIDRFLSLRVCSLPKLQLVGITALFIAAKYEEVMCPSIQNFMYMADGGYTNEEILKAEQYVLQVLGYDMS", ) self.assertEqual( alignment.sequences[41].seq, "EIFDYLRELEMETLPNPDYIDHQPDLEWKMRGILVDWLIEVHTRFRLLPETLFLAVNIIDRFLSAEVVALDRLQLVGVAAMFIASKYEEVLSPHVANFSHVADETFSDKEILDAERHILATLEYNMS", ) self.assertEqual( alignment.sequences[42].seq, "DIFEYLNELEIETMPSPTYMDRQKELAWKMRGILTDWLIEVHSRFRLLPETLFLAVNIIDRFLSLRVCSLNKLQLVGIAALFIASKYEEVMCPSVQNFVYMADGGYDEEEILQAERYILRVLEFNLA", ) self.assertEqual( alignment.sequences[43].seq, "EIFHYMQSLERKLAPPPNYMSVQQEIDWVTRHMLVDWIVQVQIHFRLLPETLFLAVNLIDRFLSIKVVSLQKVQLVGLSALLIACKYEEIHPPSIYNFAHVVQGIFTVDEIIRAERYMLMLLDFDIS", ) self.assertEqual( alignment.sequences[44].seq, "EILSHMEKLEIRFMPDYRHMSAQPYYVTEMRASVINWIVGVHTCINLLPESLFLSINVLDRFLSLQNVPASKMKLCGATALFIACKYEEIHPPTVKDLEIVLEGEWIGEDICGMEKYMLMVLQYQLG", ) self.assertEqual( alignment.sequences[45].seq, "SVCQLFQASQAVNKQQIFSVQKGLSDTMRYILIDWLVEVATMKDFTSLCLHLTVECVDRYLRRRLVPRYKLQLLGIACMVICTRFISKEILTIREAVWLTDNTYKYEDLVRVMGEIISALEGKIR", ) self.assertEqual( alignment.sequences[46].seq, "DIHGYLREMEMQNKRRPMVDYIEKVQKIVTPTMRAILVDWLVEVAVEYKLLSDTLHLSVSYIDRFLSVNPVSKSRLQLLGVSSMLIAAKYEEMDPPGVDEFCSITDHTYDKTEVVKMEADILKSLKFEMG", ) self.assertEqual( alignment.sequences[47].seq, "DIYMHLREAETRKRPSTDFMETIQKDVNPSMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNEINRQRLQLLGVACMLIAAKYEEICAPQVEEFCYITDNTYFRDEVLEMEASVLNYLKFEMT", ) self.assertEqual( alignment.sequences[48].seq, "DIYNHLRAAEAKKQPAVDYMATVQKDVNSTMRGILVDWLVEVSEEYRLVPETLYLTVNYIDRYLSGNVISRQKLQLLGVACMMIAAKYEEVCAPQVEEFCYITDNTYLKDEVLDMESAVLNYLKFEMS", ) self.assertEqual( alignment.sequences[49].seq, "DIYDNIHVAELQQRPLANYMELVQRDIDPDMRKILIDWLVEVSDDYKLVPDTLYLTVNLIDRFLSNSYIERQRLQLLGVSCMLIASKYEELSAPGVEEFCFITANTYTRPEVLSMEIQILNFVHFRLS", ) self.assertEqual( alignment.sequences[50].seq, "DIYSNIRVTELQRKPLTNYMDKLQKDINPSMRGILVDWLVEVSEEYKLVPDTLYLTVNLIDRYLSTRLIQKQKLQLLGVTCMLIASKYEEMCAPRVEEFCFITDNTYTKEEVLKMEREVLNLVHFQLS", ) self.assertEqual( alignment.sequences[51].seq, "DILTYGKEAEQRYMAKANYMERQSDINHSMRSILVDWLVEVADEYKLKRETFFLAVNYIDRFLSMMSVIRCRLQLLGAAAMFIAAKYEEIYPPDVAEFVYITDDTYTMKQVLQMEQAILKTLNFLV", ) self.assertEqual( alignment.sequences[52].seq, "DIIKYMLHRQTKNRASHECFDIQSQVNEEMRTILIDWFSDVVKEYNFQKETFHLAVSLVDRALSMFNIDKMRFQLVGTTSMMIAVKYEEIFPPEIEDFALITDNTYRVPDILLMERFLLGKFDFVVA", ) self.assertEqual( alignment.sequences[53].seq, "DILEYFRESEKKHRPKPLYMRRQKDISHNMRSILIDWLVEVSEEYKLDTETLYLSVFYLDRFLSQMAVVRSKLQLVGTAAMYIAAKYEEIYPPEVGEFVFLTDDSYTKAQVLRMEQVILKILSFDLC", ) self.assertEqual( alignment.sequences[54].seq, "EIYQYLKTAESKHRPKHGYMRKQPDITNSMRCILVDWLVEVSEEYRLHNETLYLAAAFIDRFLSQMSVLRAKLQLVGTASMFVASKYEEIYPPDVKEFVYITDDTYSIKQVLRMEHLILKVLSFDLA", ) self.assertEqual( alignment.sequences[55].seq, "DIHTYLREMEVKCKPKVGYMKRQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYSKKQVLRMEHLVLKVLAFDLA", ) self.assertEqual( alignment.sequences[56].seq, "DIHRYLRECEVKYRPKPGYMRKQPDITNCMRVILVDWLVEVGEEYKLCSETLYLAVNYLDRFLSCMSVLRGKLQLVGTAAILLAAKYEEVYPPEVDEFVYITDDTYTKKQLLRMEQHLLRVLAFDMT", ) self.assertEqual( alignment.sequences[57].seq, "EIYQYLREAEIRHRPKAHYMKKQPDITEGMRTILVDWLVEVGEEYKLRAETLYLAVNFLDRFLSCMSVLRGKLQLVGTAAMLLASKYEEIYPPEVDEFVYITDDTYTKRQLLKMEHLLLKVLAFDLT", ) self.assertEqual( alignment.sequences[58].seq, "EISTNVIAQSCKFKPNPKLIDQQPEMNPVETRSNIITFLFELSVVTRVTNGIFFHSVRLYDRYCSKRIVLRDQAKLVVATCLWLAAKTWGGCNHIINNVVIPTGGRFYGPNPRARIPRLSELVHYCGDGQVFDESMFLQMERHILDTLNWNIY", ) self.assertEqual( alignment.sequences[59].seq, "DIIHHLITREKNFLLNVHLSNQQPELRWSMRPALVNFIVEIHNGFDLSIDTLPLSISLMDSYVSRRVVYCKHIQLVACVCLWIASKFHETEDRVPLLQELKLACKNIYAEDLFIRMERHILDTLDWDIS", ) self.assertEqual( alignment.sequences[60].seq, "EMLHHLLSVEAKTLPNLSLIEQQPEIKLGMRPLLLDFLMEVITILSLSRSTFPLTVNLIDRYCSTRIVKKQHYQLLGLTSLWISCKNLDSKFKVPTLNDLRKICVDSYYKELFVEMEKHILKSLEWVVN", ) self.assertEqual( alignment.sequences[61].seq, "DIVNTLSQLESLTLVNPAMIDLQPEIQWFMRPFLLDFLIELHSSFKLQPTTLFLCLNIIDRYCAKRIVFKRHYQLVGCTALWIASKYEDKKSRVPTLKELTIMCRNAYDEEMFVQMEMHILSTLDWSIG", ) self.assertEqual( alignment.sequences[62].seq, "RVLNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLELINQEKDILEALKWDTE", ) self.assertEqual( alignment.sequences[63].seq, "IFYNILEIEPRFLTSDSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTE", ) self.assertEqual( alignment.sequences[64].seq, "DMRAFYNCMEYEEALQPNYHYFTGVQENITPFHREQAIDWIYDVAKEENCDGDVFLLAVSLIDRFMSVQNILKHDIQMIAGVALFIASKLKAPHPMTASKIAYYSDNSCPIDMILQWELLIVTTLQWETE", ) self.assertEqual( alignment.sequences[65].seq, "LENFLKVEEKHHKIPDTYFSIQKDITPPMRKIVAEWMMEVCAEENCQEEVVLLALNYMDRFLSSKSVRKTQLQILAAACLLLASKLREPSCRALSVDLLVVYTDNSIYKDDLIKWELYVLSRLGWDLS", ) self.assertEqual( alignment.sequences[66].seq, "RVLRAMLKTEETCAPSVSYFKCVQREIVPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPLKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLLVNKLKWNLA", ) self.assertEqual( alignment.sequences[67].seq, "RVLQNLLTIEERYLPQCSYFKCVQKDIQPYMRRMVATWMLEVCEEQKCEEEVFPLAMNYLDRFLAGVPTPKTHLQLLGAVCMFLASKLKETIPLTAEKLCIYTDNSVKPQELLEWELVVLGKLKWNLA", ) self.assertEqual( alignment.sequences[68].seq, "RVLQSLLRLEERYVPRASYFQCVQREIKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTDHAVSPRQLRDWEVLVLGKLKWDLA", ) self.assertEqual( alignment.sequences[69].seq, "DIFLTMREQELSRRPLFYLSPQLNERRRMLQLLKLATSAHKLSRCALHLAVYYMDRFVDYYKIRPDKLLLVAITCLHIAAQIENTDAFIPRYSEMNRLVKNAYTAFEYKAVERKILCFLNFELI", ) self.assertEqual( alignment.sequences[70].seq, "DSKQNGIEQSITKNIPITHRDLHYDKDYNLRIYCYFLIMKLGRRLNIRQYALATAHIYLSRFLIKASVREINLYMLVTTCVYLACKVEECPQYIRTLVSEARTLWPEFIPPDPTKVTEFEFYLLEELESYLI", ) self.assertEqual( alignment.sequences[71].seq, "NFWTSSHCKQLLDQEDVDKVPQADSDRGITLEEFRLVKIHMSFHIWRLAQQVKVRQRVIATAVTYFRRVYTRKSMTEYDPRLVAPTCLYLASKVEESTVQARLLVFYIKKMCASDEKYRFEIKDILEMEMKLLEALDYYLV", ) self.assertEqual( alignment.sequences[72].seq, "DKIWYFSNDQLANSPSRRCGIKGDDELQYRQMTAYLIQEMGQRLQVSQLCINTAIVYMHRFYAFHSFTHFHRNSMASASLFLAAKVEEQPRKLEHVIRAANKCLPPTTEQNYAELAQELVFNENVLLQTLGFDVA", ) self.assertEqual( alignment.sequences[73].seq, "IIPWFFSREEIERNSPSRRDGIDLKTETRLRDSYCTFLEILGERLKVPQVTIATAIFFCHRFFLRQSHAKNDRQTIATVCMLLAGKVEETPVTLEDVIIASYERIHKKDLAGAQRKEVYDQQKELVLIGEELVLSTLNFDLC", ) self.assertEqual( alignment.sequences[74].seq, "DVMSMQQHVELNKAQTMKPIDYRKMNKPGVVPMYIFECAAKLKMKPLTAACAAIVFHRFFREVKASDYDEFLIAAGSLYLAGKIKEDESVKIRDVINVAYCTLNRGNDPVDLNDEYWSMRDAIVQAELLITRTLCFDLN", ) self.assertEqual( alignment.sequences[75].seq, "DIIKFLTDTTLRVVPSSNYPTPPGSPGEKHLTRLPSLMTFITRLVRYTNVYTPTLLTAACYLNKLKRILPRDATGLPSTIHRIFLACLILSAKFHNDSSPLNKHWARYTDGLFTLEDINLMERQLLQLLNWDLR", ) self.assertEqual( alignment.sequences[76].seq, "EMVQYLASTTASIIKIKKTNSMIDIALPAPPLTKFINRLIKHSNVQTPTLMATSVYLAKLRSIIPSNVYGIETTRHRIFLGCLILAAKTLNDSSPLNKHWAEYTDGLLILREVNTIERELLEYFDWDVT", ) self.assertEqual( alignment.sequences[77].seq, "EMIQFLATSTASIIKIRENNNPIQGCRPPDLSIFIKNVVIQSNVQTPTLMATSVYLNKLKSVIPKNVYGINTTRHRIFLGCLILAAKTLNDSSPWNKHWTTYTEGLLRIREVNTIERELLEYLNWDVR", ) self.assertEqual( alignment.sequences[78].seq, "RVAESNDLTRRVATQSQRVSVFHGLSRPTITIQSYLERIFKYANCSPSCFVVAYVYLDRFTHRQPSLPINSFNVHRLLITSVMVAAKFLDDLYYNNAYYAKVGGISTKEMNFLELDFLFGLGFELN", ) self.assertEqual( alignment.sequences[79].seq, "DIFDEKLHPLTHDQVPDNYDTHNPEHRQIYKFVRTLFNAAQLTAECAIITLVYLERLLTYAELDVGPCNWKRMVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQFNIN", ) self.assertEqual( alignment.sequences[80].seq, "DSIACFIEDERHFVPGHDYLSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYARRLPETSGWPMQLLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSVLDWRLR", ) self.assertEqual( alignment.sequences[81].seq, "DRIKEMLVREIEFCPGTDYVKRLLSGDLDLSVRNQALDWILKVCAHYHFGHLCICLSMNYLDRFLTSYELPKDKDWAAQLLAVSCLSLASKMEETDVPHIVDLQVEDPKFVFEAKTIKRMELLVVTTLNWRLQ", ) self.assertEqual( alignment.sequences[82].seq, "EIIMEMVEKEKQHLPSDDYIKRLRSGDLDLNVGRRDALNWIWKACEVHQFGPLCFCLAMNYLDRFLSVHDLPSGKGWILQLLAVACLSLAAKIEETEVPMLIDLQVGDPQFVFEAKSVQRMELLVLNKLKWRLR", ) self.assertEqual( alignment.sequences[83].seq, "EELTSLFSKETEYEISYNVLEKNQSFISSRRESVEWILKTTAYYSFSAQTGFLAVNYFDRFLLFSFNQSLNHKPWMNQLVAVTCLSLAAKVEETDVPLLLDLQVEESGFLFESKTIQRMEMLILSTLKWKMN", ) self.assertEqual( alignment.sequences[84].seq, "DELATLLSKENEFHLGFQSLISDGSLMGARKEALDWMLRVIAYYGFTATTAVLAVNYFDRFVSGWCFQKDKPWMSQLAAVACLSIAAKVEETQVPLLLDLQVADSRFVFEAKTIQRMELLVLSTLKWKMN", ) self.assertEqual( alignment.sequences[85].seq, "DELSTLISKQEPCLYDEILDDEFLVLCREKALDWIFKVKSHYGFNSLTALLAVNYFDRFITSRKFQTDKPWMSQLTALACLSLAAKVEEIRVPFLLDFQVEEARYVFEAKTIQRMELLVLSTLDWRMH", ) self.assertEqual( alignment.sequences[86].seq, "TLPHSLFLVEFQHMPSSHYFHSLKSSAFLLSNRNQAISSITQYSRKFDDPSLTYLAVNYLDRFLSSEDMPQSKPWILKLISLSCVSLSAKMRKPDMSVSDLPVEGEFFDAQMIERMENVILGALKWRMR", ) self.assertEqual( alignment.sequences[87].seq, "DVWRLMCHRDEQDSRLRSISMLEQHPGLQPRMRAILLDWLIEVCEVYKLHRETFYLAVDYLDRYLHVAHKVQKTHLQLIGITCLFVAAKVEEIYPPKIGEFAYVTDGACTERDILNHEKILLQALDWDIS", ) self.assertEqual( alignment.sequences[88].seq, "EVWQNMLQKENRYVHDKHFQVLHSDLEPQMRSILLDWLLEVCEVYTLHRETFYLAQDFFDRFMLTQKDVNKNMLQLIGITSLFIASKLEEIYAPKLQEFAYVTDGACSEVDILKMELNILKALKWELC", ) self.assertEqual( alignment.sequences[89].seq, "DVWKNMINKEETYVRDKLYMQRHPLLQPKMRTILLDWLMEVCEVYKLYRETFYLAQDFFDRFMATQQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACTEDEILSMELIIMKALNWNLN", ) self.assertEqual( alignment.sequences[90].seq, "EVWRIMLNKEKTYLRDEHFLQRHPLLQARMRAVLLDWLMEVCEVYKLHRETFYLAQDFFDRYMASQHNIIKTLLQLIGISALFIASKLEEIYPPKLHQFAYVTDGACSGDEILTMELMMMKALKWRLS", ) self.assertEqual( alignment.sequences[91].seq, "EVWNNLLGKDKLYLRDTRVMERHPNLQPKMRAILLDWLMEVCEVYKLHRETFYLGQDYFDRFMATQENVLKTTLQLIGISCLFIAAKMEEIYPPKVHQFAYVTDGACTEDDILSMEIIIMKELNWSLS", ) self.assertEqual( alignment.sequences[92].seq, "DVWRNMLNKDRTYLRDKNFFQKHPQLQPNMRAILLDWLMEVCEVYKLHRETFYLGQDFFDRFMATQKNVIKSRLQLIGITSLFIAAKLEEIYPPKLHQFAFITDGACTEDEITSMELIIMKDLDWCLS", ) self.assertEqual( alignment.sequences[93].seq, "EVWTIMTRKEALCPRKHDCLKSHPSLGERMRAILLDWLIEVCEVYRLHRESFYLAADFVDRYLAAKENVPKTKLQLIGITSLFVAAKLEEIYPPKLHEFAYVTDGACTDDQILDQELIMLMTLNWDLT", ) self.assertEqual( alignment.sequences[94].seq, "KVWSLMVKRDEIPRATRFLLGNHPDMDDEKRRILIDWMMEVCESEKLHRETFHLAVDYVDRYLESSNVECSTDNFQLVGTAALFIAAKYEEIYPPKCIDFAHLTDSAFTCDNIRTMEVLIVKYIGWSLG", ) self.assertEqual( alignment[0], "GIFDYYRHREV---HFRVRKYL--HKHPE---VDV-KTRAILIDW---MVEIQETFELNHETLYNAVKLTDMYLCKTK-NVDKN------TIQKLACVAIFIAAKY-----------------------DERS--PPLVDDLIYLS--------------GD--RFSRDELLAMERELFATVGYDLG", ) self.assertEqual( alignment[1], "DIFDYYRDREV---KFRIPDYM--FQQTD---LTP-SMRAILVDW---LVEVQQSFELNHETLYMAVKLIDIFSS-KV-TIKRN------KLQLIGAVALNLACKF-----------------------EERC--PPMLDDFVYVC--------------DD--AYPRQEFLKMEELVFQAVGFDIG", ) self.assertEqual( alignment[2], "DIFNYLKVREA---EFPIADYM--PRQIH---LTT-WMRTLLVDW---MVEVQETFELNHETLYLAVKIVDLYLC-RE-VINKE------KLQLLGAAAFFIACKY-----------------------DERQ--PPLIEDFLYIC--------------DG--AYNHDELVRMERETLRVIKYDLG", ) self.assertEqual( alignment[3], "EIFDYMREREE---KFLLPDYM--EKQSD---ISR-DMRAILVDW---MVEVQENFELNHETLYLAVKLVDHYLV-EV-VSMRD------KLQLIGSTAVLIASKF-----------------------EERC--PPCVDDFLYIC--------------DD--AYKREELIAMETSILRTLNFDIN", ) self.assertEqual( alignment[4], "DIYQFYWTAEA--LNPALGHYL--SAHAE---VSP-VTRGILINW---LIEVHFKFDLMHETLYLTMDLLDRYLS-QV-PIHKN------EMQLIGLTALLLASKY-----------------------EDYW--HPRIKDLISIS--------------AE--SYTREQILGMERSMLKQLKFRLN", ) self.assertEqual( alignment[5], "DIYKFYKLVEN--ESRP-HDYI--GSQPE---INE-RMRAILVDW---LIDVHTKFELSLETLYLTINIIDRFLA-VK-TVPRR------ELQLVGISAMLMASKY-----------------------EEIW--PPEVNDFVCLS--------------DR--AYTHEHILTMEKTILNKLEWTLT", ) self.assertEqual( alignment[6], "DIYSFYKSVES--EWRP-RDYM--ASQPD---INE-KMRLILVEW---LIDVHVRFELNPETFYLTVNILDRFLS-VK-PVPRK------ELQLVGLSALLMSAKY-----------------------EEIW--PPQVEDLVDIA--------------DH--AYSHKQILVMEKTILSTLEWYLT", ) self.assertEqual( alignment[7], "DMYSFYKEVEK--ESQP-KMYM--HIQTE---MNE-KMRAILIDW---LLEVHIKFELNLETLYLTVNIIDRFLS-VK-AVPKR------ELQLVGISALLIASKY-----------------------EEIW--PPQVNDLVYVT--------------DN--AYSSRQILVMEKAILGNLEWYLT", ) self.assertEqual( alignment[8], "DIYKFYKLTED--ENRP-CDYM--DSQPE---IND-RVRAILVDW---LIEAHKRFELRPESLYLTVNIMDRFLS-EE-TVPRR------ELQLLCISSMLIACKY-----------------------EEIW--APEVNDFLTIT--------------DN--AYVRDQILLMEKVILGKLEWYLT", ) self.assertEqual( alignment[9], "DIYKFYKETEE--DGCV-HDYM--GSQPD---INA-KMRSILVDW---LIEVHRKFELMPETLYLTLNIVDRFLS-VK-AVPRR------ELQLVGISSMLIASKY-----------------------EEIW--APEVNDFVCIS--------------DN--AYVSEQVLMMEKTILRKLEWYLT", ) self.assertEqual( alignment[10], "DIFKFYRTVEE--EGGI-KDYI--GSQPE---INE-KMRSILIDW---LVDVHRKFELMPETLYLTINLVDRFLS-LT-MVHRR------ELQLLGLGAMLIACKY-----------------------EEIW--APEVNDFVCIS--------------DN--AYNRKQVLAMEKSILGQVEWYIT", ) self.assertEqual( alignment[11], "DIYRFYKSTEG--TCLPLSSYM--SSQAE---ISE-RMRAILIDW---IIEVQYRLTLMPETLYLTVYIIDQYLS-ME-SVPRK------ELQLVGISAMLIASKY-----------------------EEIW--APLVKDLMCLC--------------DN--AFTRDQILTKEKAILDMLHWNLT", ) self.assertEqual( alignment[12], "DIYTFYKIAQH--DRRP-CDYI--DTQVE---INP-KMRAILAGW---IIEVHHKFELMPETLYLTMYIIDQYLS-LQ-PVLRR------ELQLVGVSAMLIACKY-----------------------EEIW--APEVNDFILIS--------------DS--AYSREQILSMEKGILNSLEWNLT", ) self.assertEqual( alignment[13], "DIYTFYKTAQH--ESRP-IDYM--GNQPE---LSP-RMRSILADW---LIESHRRFQLMPETLYLTIYIVDRYLS-LQ-PTPRR------ELQLVGVAALLIACKY-----------------------EEIW--APEVNDLIHIA--------------DG--AFNRSQILAAEKAILNSMEWNLT", ) self.assertEqual( alignment[14], "ELYKFYRENEE--MSCVQPDYM--SSQGD---INE-KMRAILIDW---LIEVHHKFELMDETLFLTVNIVDRFLE-KQ-VVPRK------KLQLVGVTAMLLACKY-----------------------EEVA--VPVVEDLVLIS--------------DR--AYTKGQILEMEKLILNTLQFNMS", ) self.assertEqual( alignment[15], "DLYAFYRTMER--FSCVPVDYM--MQQID---LNE-KMRAILIDW---LIEVHDKFDLINETLFLTVNLIDRFLS-KQ-NVMRK------KLQLVGLVALLLACKY-----------------------EEVS--VPVVEDLVLIS--------------DK--AYTRNDVLEMEKTMLSTLQFNIS", ) self.assertEqual( alignment[16], "DLFANYRTMEV--NSCASPYYM--AQQAD---INE-RMRSILIDW---LIEVHHKFELREETLFLTVNLIDRFLE-KQ-GIVRK------KLQLVGLVAMLLACKY-----------------------EEVC--APLVEDLVLIS--------------DK--AYTRKEVLEMESMMLNTLQFNMS", ) self.assertEqual( alignment[17], "EIYRFYRKTEG--ASCVPTNYM--SSQTD---INE-KMRGILIDW---LIEVHYKLELLEETLFLTVNIIDRFLA-RE-NVVRK------KLQLAGVTAMLLACKY-----------------------EEVS--VPVVEDLILIC--------------DR--AYTRADILEMERRIVNTLNFNMS", ) self.assertEqual( alignment[18], "DIYCFYKKNEC--RSCVPPNYM--ENQHD---INE-RMRGILFDW---LIEVHYKFELMEETLYLTINLIDRFLAVHQ-HIARK------KLQLVGVTAMLLACKY-----------------------EEVS--VPVVDDLILIS--------------DK--AYTRTEILDMEKLMANTLQFNFC", ) self.assertEqual( alignment[19], "EIFAYYREKEQ--IDKIDKDYI--KNQYH---INE-RMRAILVDW---MMAVHVRFKLLSETFFLSVNIVDRYLA-KV-MIPVT------KLQLVGITAILLACKY-----------------------EEIY--SPQIKDFVHTS--------------DD--ACTHAEVIDMERQILSTLQFHMS", ) self.assertEqual( alignment[20], "DIYNYLVHHEK--KYVLDDSFI------NGGNVNS-KMRRILVDW---LIQVHLRFHLTPETLHLTIFVLDRIIV-KN-IVSKA------EFQLLGVAALFVASKF-----------------------EDIY--LPDILEYEMIT--------------DN--TFSKKQIMAMEQTILNALNFDLS", ) self.assertEqual( alignment[21], "DIYKYLVHHEK--KYLLEECFM------EGGEPTP-KMRRILVDW---LVQVHVRFHLTPETLHLTVFILDRMLQ-KK-VTSKA------DLQLLGISAMFVASKF-----------------------EEVY--LPDIHDYEFIT--------------EN--TYSKKQILAMEQTILNSLNFDLS", ) self.assertEqual( alignment[22], "DIYKYLTELEE--KYSIEPDHL--KKQTV---ITG-KMRATLIDW---LVEVQRQFSLVLETFHLTVGIIDRYLQVVP-NVQRN------QLQLVGVTAMFIASKY-----------------------EEIY--APDVGDFVYVT--------------DN--AYTKSDVFRCERDIMCKLGFCLA", ) self.assertEqual( alignment[23], "DIYDYLYQVEL--EQPIHKDHL--AGQKE---VSH-KMRAVLIDW---INEVHLQFHLAAETFQLAVAIIDRYLQVVK-DTKRT------YLQLVGVTALFIATKY-----------------------EELF--PPAIGDFVFIT--------------DD--TYTARQIRQMELQIFKAIDCNLS", ) self.assertEqual( alignment[24], "DIYCYLRSLEN--AQAVRQNYL--HG-QE---VTG-NMRAILIDW---LVQVQMKFRLLQETMFMTVGIIDRFLQ-DH-PVPKN------QLQLVGVTAMFLAAKY-----------------------EEMY--PPEIGDFTFVT--------------DH--TYTKAQIRDMEMKVLRVLKFAIG", ) self.assertEqual( alignment[25], "DIYAYLRQLEE--EQSVRPKYL--QG-RE---VTG-NMRAILIDW---LIQVQMKFRLLQETMYMTVSIIDRFMQ-NS-CVPKK------MLQLVGVTAMFIASKY-----------------------EEMY--PPEIGDFAFVT--------------NN--TYTKHQIRQMEMKILRVLNFSLG", ) self.assertEqual( alignment[26], "DIYNYLKQLEV--QQSVRPCYL--EG-KE---INE-RMRAILVDW---IVQVHSRFQLLQETLYMGIAIMDRFLQ-VQ-PVSRS------KLQLVGVTSLLVASKY-----------------------EEMY--TPEVADFVYIT--------------DN--AYTASQIREMEMIILRVLNFDLG", ) self.assertEqual( alignment[27], "DIYQYLRQLEV--LQSINPHFL--DG-RD---ING-RMRAILVDW---LVQVHSKFRLLQETLYMCVGIMDRFLQ-VQ-PVSRK------KLQLVGITALLLASKY-----------------------EEMF--SPNIEDFVYIT--------------DN--AYTSSQIREMETLILKELKFELG", ) self.assertEqual( alignment[28], "DIYLYLRQLEL--QQSVRPHYL--DG-KT---ING-RMRAILVDW---LVQVHSRFQLLQETLYMCVAVMDRFLQ-SH-PVPRK------RLQLVGVTALLLASKY-----------------------EEMY--SPDIADFVYIT--------------DN--AYNSAEVREMEITILKELNFDLG", ) self.assertEqual( alignment[29], "EILQHLLIEEN--KYTI-NQYMTPEQQPD---INI-KMRAILVDW---LIDVHAKFKLKDETLYITISLIDRYLA-LA-QVTRM------RLQLVGVAALFIACKY-----------------------EEIY--PPALKDFVYIT--------------DN--AYVKSDVLEMEGLMLQALNFNIC", ) self.assertEqual( alignment[30], "EIYTYLLTQEE--KYLVSNNYMNEQQQPD---LNA-RMRAILLDW---LIDVHLKFKLRDETLYVTTYLIDRFLN-FK-TTTRQ------QLQLVGVASLFIACKY-----------------------EEIY--PPDLKDFVYIT--------------DN--AYTKQDVLEMEGQILQTLDFSIT", ) self.assertEqual( alignment[31], "EIFSYYYELET--RMLPDPQYL--FKQTL---LKP-RMRSILVDW---LVEMHLKFKLLPESLFLAVNVMDRFMS-VE-VVQID------KLQLLATAALFTAAKY-----------------------EEVF--SPSVKNYAYFT--------------DG--SYTPEEVVQAEKYMLTILNFDLN", ) self.assertEqual( alignment[32], "EIFAFLYRREL--ETLPSHNYL--LDKTSKYYLRP-SMRTILVDW---LVEVHEKFQCYPETLFLSINLMDRFLA-KN-KVTMN------KLQLLAVTSLFIAAKF-----------------------EEVN--LPKLAEYAYIT--------------DG--AASKNDIKNAEMFMLTSLEFNIG", ) self.assertEqual( alignment[33], "SIFSHLYEKEI--QMLPTHNYL--MDTQSPYHLKS-SMRALLIDW---LVEVHEKFHCLPETLFLAINLLDRFLS-QN-VVKLN------KLQLLCITCLFIACKF-----------------------EEVK--LPKITNFAYVT--------------DG--AATVEGIRKAELFVLSSLGYNIS", ) self.assertEqual( alignment[34], "DIFDYLHHLEI--ITLPNKANL--YKHKN---IK--QNRDILVNW---IIKIHNKFGLLPETLYLAINIMDRFLC-EE-VVQLN------RLQLVGTSCLFIASKY-----------------------EEIY--SPSIKHFAYET--------------DG--ACSVEDIKEGERFILEKLDFQIS", ) self.assertEqual( alignment[35], "DIFEYLHQLEV--ITLPKKEDL--YQHRN---IH--QNRDILVNW---LVKIHNKFGLLPETLYLAINIMDRFLG-KE-LVQLD------KLQLVGTSCLFIASKY-----------------------EEVY--SPSIKHFASET--------------DG--ACTEDEIKEGEKFILKTLKFNLN", ) self.assertEqual( alignment[36], "EIFNYLHELEN--KFTPDPNYM--DFQDD---LKW-EMRAVLIDW---VVQVHARFNLFSETLYLTVNYIDRFLS-KR-RVSLS------RFQLVGAVALFIAAKY-----------------------EEIN--CPTVQEIAYMA--------------DN--AYSIDEFLKAERFMIDVLEFDLG", ) self.assertEqual( alignment[37], "EIFEYMRKLED--LYKPNPYYM--DKQPE---LRW-SFRSTLIDW---IVQVHEKFQLLPETLYLCINIIDRYLC-KE-VVPVN------KFQLVGAASLFIAAKY-----------------------EEIN--CPTIKDFVYMS--------------EN--CYSRNDLLDAERTILNGLEFELG", ) self.assertEqual( alignment[38], "DIFYYLRELEV--KYRPNPYYM--QNQVE---LTW-PFRRTMIDW---LVQLHFRFQLLPETLYLTINIVDRFLS-KK-TVTLN------RFQLVGVSALFIAAKF-----------------------EEIN--CPTLDDLVYML--------------EN--TYTRDDIIRAEQYMIDTLEFEIG", ) self.assertEqual( alignment[39], "EIFEYIRKLDL--KCLPNPKYM--DQQKE---LTW-KMREILNEW---LVEIHSNFCLMPETLYLAVNIIDRFLS-RR-SCSLS------KFQLTGITALLIASKY-----------------------EEVM--CPSIQNFVYMT--------------DG--AFTVEDVCVAERYMLNVLNFDLS", ) self.assertEqual( alignment[40], "EIMSYMRELEV--LTLPLPDYM--DRQKE---LQW-KMRGILVDW---LIEVHAKFRLLPETLFLSVNIIDRFLS-LR-VCSLP------KLQLVGITALFIAAKY-----------------------EEVM--CPSIQNFMYMA--------------DG--GYTNEEILKAEQYVLQVLGYDMS", ) self.assertEqual( alignment[41], "EIFDYLRELEM--ETLPNPDYI--DHQPD---LEW-KMRGILVDW---LIEVHTRFRLLPETLFLAVNIIDRFLS-AE-VVALD------RLQLVGVAAMFIASKY-----------------------EEVL--SPHVANFSHVA--------------DE--TFSDKEILDAERHILATLEYNMS", ) self.assertEqual( alignment[42], "DIFEYLNELEI--ETMPSPTYM--DRQKE---LAW-KMRGILTDW---LIEVHSRFRLLPETLFLAVNIIDRFLS-LR-VCSLN------KLQLVGIAALFIASKY-----------------------EEVM--CPSVQNFVYMA--------------DG--GYDEEEILQAERYILRVLEFNLA", ) self.assertEqual( alignment[43], "EIFHYMQSLER--KLAPPPNYM--SVQQE---IDW-VTRHMLVDW---IVQVQIHFRLLPETLFLAVNLIDRFLS-IK-VVSLQ------KVQLVGLSALLIACKY-----------------------EEIH--PPSIYNFAHVV--------------QG--IFTVDEIIRAERYMLMLLDFDIS", ) self.assertEqual( alignment[44], "EILSHMEKLEI--RFMPDYRHM--SAQPY---YVT-EMRASVINW---IVGVHTCINLLPESLFLSINVLDRFLS-LQ-NVPAS------KMKLCGATALFIACKY-----------------------EEIH--PPTVKDLEIVL--------------EG--EWIGEDICGMEKYMLMVLQYQLG", ) self.assertEqual( alignment[45], "SVCQLFQASQA----VNKQQIF--SVQKG---LSD-TMRYILIDW---LVEVATMKDFTSLCLHLTVECVDRYLR-RR-LVPRY------KLQLLGIACMVICTRFI---------------------SKEIL----TIREAVWLT--------------DN--TYKYEDLVRVMGEIISALEGKIR", ) self.assertEqual( alignment[46], "DIHGYLREMEMQNKRRPMVDYI-EKVQKI---VTP-TMRAILVDW---LVEVAVEYKLLSDTLHLSVSYIDRFLS-VN-PVSKS------RLQLLGVSSMLIAAKY-----------------------EEMD--PPGVDEFCSIT--------------DH--TYDKTEVVKMEADILKSLKFEMG", ) self.assertEqual( alignment[47], "DIYMHLREAET--RKRPSTDFM-ETIQKD---VNP-SMRAILIDW---LVEVAEEYRLVPDTLYLTVNYIDRYLS-GN-EINRQ------RLQLLGVACMLIAAKY-----------------------EEIC--APQVEEFCYIT--------------DN--TYFRDEVLEMEASVLNYLKFEMT", ) self.assertEqual( alignment[48], "DIYNHLRAAEA--KKQPAVDYM-ATVQKD---VNS-TMRGILVDW---LVEVSEEYRLVPETLYLTVNYIDRYLS-GN-VISRQ------KLQLLGVACMMIAAKY-----------------------EEVC--APQVEEFCYIT--------------DN--TYLKDEVLDMESAVLNYLKFEMS", ) self.assertEqual( alignment[49], "DIYDNIHVAEL--QQRPLANYM-ELVQRD---IDP-DMRKILIDW---LVEVSDDYKLVPDTLYLTVNLIDRFLS-NS-YIERQ------RLQLLGVSCMLIASKY-----------------------EELS--APGVEEFCFIT--------------AN--TYTRPEVLSMEIQILNFVHFRLS", ) self.assertEqual( alignment[50], "DIYSNIRVTEL--QRKPLTNYM-DKLQKD---INP-SMRGILVDW---LVEVSEEYKLVPDTLYLTVNLIDRYLS-TR-LIQKQ------KLQLLGVTCMLIASKY-----------------------EEMC--APRVEEFCFIT--------------DN--TYTKEEVLKMEREVLNLVHFQLS", ) self.assertEqual( alignment[51], "DILTYGKEAEQ--RYMAKANYM--ERQSD---INH-SMRSILVDW---LVEVADEYKLKRETFFLAVNYIDRFLS-MM-SVIRC------RLQLLGAAAMFIAAKY-----------------------EEIY--PPDVAEFVYIT--------------DD--TYTMKQVLQMEQAILKTLNF-LV", ) self.assertEqual( alignment[52], "DIIKYMLHRQT--KNRASHECF--DIQSQ---VNE-EMRTILIDW---FSDVVKEYNFQKETFHLAVSLVDRALS-MF-NIDKM------RFQLVGTTSMMIAVKY-----------------------EEIF--PPEIEDFALIT--------------DN--TYRVPDILLMERFLLGKFDFVVA", ) self.assertEqual( alignment[53], "DILEYFRESEK--KHRPKPLYM--RRQKD---ISH-NMRSILIDW---LVEVSEEYKLDTETLYLSVFYLDRFLS-QM-AVVRS------KLQLVGTAAMYIAAKY-----------------------EEIY--PPEVGEFVFLT--------------DD--SYTKAQVLRMEQVILKILSFDLC", ) self.assertEqual( alignment[54], "EIYQYLKTAES--KHRPKHGYM--RKQPD---ITN-SMRCILVDW---LVEVSEEYRLHNETLYLAAAFIDRFLS-QM-SVLRA------KLQLVGTASMFVASKY-----------------------EEIY--PPDVKEFVYIT--------------DD--TYSIKQVLRMEHLILKVLSFDLA", ) self.assertEqual( alignment[55], "DIHTYLREMEV--KCKPKVGYM--KRQPD---ITN-SMRAILVDW---LVEVGEEYKLQNETLHLAVNYIDRFLS-SM-SVLRG------KLQLVGTAAMLLASKF-----------------------EEIY--PPEVAEFVYIT--------------DD--TYSKKQVLRMEHLVLKVLAFDLA", ) self.assertEqual( alignment[56], "DIHRYLRECEV--KYRPKPGYM--RKQPD---ITN-CMRVILVDW---LVEVGEEYKLCSETLYLAVNYLDRFLS-CM-SVLRG------KLQLVGTAAILLAAKY-----------------------EEVY--PPEVDEFVYIT--------------DD--TYTKKQLLRMEQHLLRVLAFDMT", ) self.assertEqual( alignment[57], "EIYQYLREAEI--RHRPKAHYM--KKQPD---ITE-GMRTILVDW---LVEVGEEYKLRAETLYLAVNFLDRFLS-CM-SVLRG------KLQLVGTAAMLLASKY-----------------------EEIY--PPEVDEFVYIT--------------DD--TYTKRQLLKMEHLLLKVLAFDLT", ) self.assertEqual( alignment[58], "EISTNVIAQSC--KFKPNPKLI--DQQPE---MNPVETRSNIITF---LFELSVVTRVTNGIFFHSVRLYDRYCS-KR-IVLRD------QAKLVVATCLWLAAKTWGGCNHIINNVVIPTGGRFYGPNPRAR--IPRLSELVHYC--------------GDGQVFDESMFLQMERHILDTLNWNIY", ) self.assertEqual( alignment[59], "DIIHHLITREK--NFLLNVHLS--NQQPE---LRW-SMRPALVNF---IVEIHNGFDLSIDTLPLSISLMDSYVS-RR-VVYCK------HIQLVACVCLWIASKF-----------------------HETEDRVPLLQELKLAC--------------KN--IYAEDLFIRMERHILDTLDWDIS", ) self.assertEqual( alignment[60], "EMLHHLLSVEA--KTLPNLSLI--EQQPE---IKL-GMRPLLLDF---LMEVITILSLSRSTFPLTVNLIDRYCS-TR-IVKKQ------HYQLLGLTSLWISCKN-----------------------LDSKFKVPTLNDLRKIC--------------VD--SYYKELFVEMEKHILKSLEWVVN", ) self.assertEqual( alignment[61], "DIVNTLSQLES--LTLVNPAMI--DLQPE---IQW-FMRPFLLDF---LIELHSSFKLQPTTLFLCLNIIDRYCA-KR-IVFKR------HYQLVGCTALWIASKY-----------------------EDKKSRVPTLKELTIMC--------------RN--AYDEEMFVQMEMHILSTLDWSIG", ) self.assertEqual( alignment[62], "RVLNNLKLREL---LLPKFTSL-WEIQTE---VTV-DNRTILLTW---MHLLCESFELDKSVFPLSVSILDRYLC-KK-QGTKK------TLQKIGAACVLIGSKI-----------------------RTVK--PMTVSKLTYLS--------------CD--CFTNLELINQEKDILEALKWDTE", ) self.assertEqual( alignment[63], "-IFYNILEIEP--RFLTSDSVFGTFQQS----LTS-HMRKLLGTW---MFSVCQEYNLEPNVVALALNLLDRLLL-IK-QVSKE------HFQKTGSACLLVASKL-----------------------RSLT--PISTSSLCYAA--------------AD--SFSRQELIDQEKELLEKLAWRTE", ) self.assertEqual( alignment[64], "DMRAFYNCMEYEEALQPNYHYF-TGVQEN---ITP-FHREQAIDW---IYDVAKEENCDGDVFLLAVSLIDRFMS-VQ-NILKH------DIQMIAGVALFIASKL-----------------------KAPH--PMTASKIAYYS--------------DN--SCPIDMILQWELLIVTTLQWETE", ) self.assertEqual( alignment[65], "--LENFLKVEEKHHKIPDTYF---SIQKD---ITP-PMRKIVAEW---MMEVCAEENCQEEVVLLALNYMDRFLS-SK-SVRKT------QLQILAAACLLLASKL-----------------------REPSCRALSVDLLVVYT--------------DN--SIYKDDLIKWELYVLSRLGWDLS", ) self.assertEqual( alignment[66], "RVLRAMLKTEE--TCAPSVSYF-KCVQRE---IVP-SMRKIVATW---MLEVCEEQKCEEEVFPLAMNYLDRFLS-LE-PLKKS------RLQLLGATCMFVASKM-----------------------KETI--PLTAEKLCIYT--------------DN--SIRPEELLQMELLLVNKLKWNLA", ) self.assertEqual( alignment[67], "RVLQNLLTIEE--RYLPQCSYF-KCVQKD---IQP-YMRRMVATW---MLEVCEEQKCEEEVFPLAMNYLDRFLA-GV-PTPKT------HLQLLGAVCMFLASKL-----------------------KETI--PLTAEKLCIYT--------------DN--SVKPQELLEWELVVLGKLKWNLA", ) self.assertEqual( alignment[68], "RVLQSLLRLEE--RYVPRASYF-QCVQRE---IKP-HMRKMLAYW---MLEVCEEQRCEEEVFPLAMNYLDRYLS-CV-PTRKA------QLQLLGAVCMLLASKL-----------------------RETT--PLTIEKLCIYT--------------DH--AVSPRQLRDWEVLVLGKLKWDLA", ) self.assertEqual( alignment[69], "DIFLTMREQEL-------------SRRPLFYLSPQLNERRRMLQL---LKLATSAHKLSRCALHLAVYYMDRFVD-YY-KIRPD------KLLLVAITCLHIAAQI-----------------------ENTDAFIPRYSEMNRLV--------------KN--AYTAFEYKAVERKILCFLNFELI", ) self.assertEqual( alignment[70], "DSKQNGIEQSITKNIPITHRDLHYDKDYN--------LRIYCYFL---IMKLGRRLNIRQYALATAHIYLSRFLI-KA-SVREI------NLYMLVTTCVYLACKV-----------------------EEC---PQYIRTLVSEART----------LWPEFIPPDPTKVTEFEFYLLEELESYLI", ) self.assertEqual( alignment[71], "----NFWTSSHCKQLLDQEDVDKVPQADSDRGITLEEFRLVKIHMSFHIWRLAQQVKVRQRVIATAVTYFRRVYT-RK-SMTEY------DPRLVAPTCLYLASKV-----------------------EES---TVQARLLVFYIKKM--------CASDEKYRFEIKDILEMEMKLLEALDYYLV", ) self.assertEqual( alignment[72], "DKIWYFSNDQL-ANSPSRRCGIKGDDELQ--------YRQMTAYL---IQEMGQRLQVSQLCINTAIVYMHRFYA-FH-SFTHF------HRNSMASASLFLAAKV-----------------------EEQ---PRKLEHVIRAANKCL------PPTTEQNYAELAQELVFNENVLLQTLGFDVA", ) self.assertEqual( alignment[73], "IIPWFFSREEIERNSPSRRDGIDLKTETR--------LRDSYCTF---LEILGERLKVPQVTIATAIFFCHRFFL-RQ-SHAKN------DRQTIATVCMLLAGKV-----------------------EET---PVTLEDVIIASYERIHKKDLAGAQRKEVYDQQKELVLIGEELVLSTLNFDLC", ) self.assertEqual( alignment[74], "DVMSMQQHVELNKAQTMKPIDYRKMNKPG-----------VVPMY---IFECAAKLKMKPLTAACAAIVFHRFFR----EVKASD----YDEFLIAAGSLYLAGKI-----------------------KEDE--SVKIRDVINVAYCTLNRGNDPVDLNDEYWSM-RDAIVQAELLITRTLCFDLN", ) self.assertEqual( alignment[75], "DIIKFLTDTTL--RVVPSSNYPTPPGSPG---EKHLTRLPSLMTF---ITRLVRYTNVYTPTLLTAACYLNKLKR----ILPRDATGLPSTIHRIFLACLILSAKF-----------------------HNDS--SPLNKHWARYT--------------DG--LFTLEDINLMERQLLQLLNWDLR", ) self.assertEqual( alignment[76], "EMVQYLASTTASIIKIKKTNSMIDIALPA----------PPLTKF---INRLIKHSNVQTPTLMATSVYLAKLRS----IIPSNVYGIETTRHRIFLGCLILAAKT-----------------------LNDS--SPLNKHWAEYT--------------DG--LLILREVNTIERELLEYFDWDVT", ) self.assertEqual( alignment[77], "EMIQFLATSTASIIKIRENNNPIQGCRP-----------PDLSIF---IKNVVIQSNVQTPTLMATSVYLNKLKS----VIPKNVYGINTTRHRIFLGCLILAAKT-----------------------LNDS--SPWNKHWTTYT--------------EG--LLRIREVNTIERELLEYLNWDVR", ) self.assertEqual( alignment[78], "RVAESNDLTRRVATQSQRVSVFHGLSRPT----------ITIQSY---LERIFKYANCSPSCFVVAYVYLDRFTH-RQPSLPINS----FNVHRLLITSVMVAAKF--------------------------------LDDLYYNNAYY-------AKVG----GISTKEMNFLELDFLFGLGFELN", ) self.assertEqual( alignment[79], "DIFD------------EKLHPLTHDQVPDNYDTHNPEHRQ-IYKF---VRTLFNAAQLTAECAIITLVYLERLLTYAELDVGPC------NWKRMVLGAILLASKV--------------------------------WDDQAVWNVDYC------QILK----DITVEDMNELERQFLELLQFNIN", ) self.assertEqual( alignment[80], "DSIACFIEDER--HFVPGHDYLSRFQTRS---LDA-SAREDSVAW---ILKVQAYYNFQPLTAYLAVNYMDRFLY-AR-RLPETS---GWPMQLLAVACLSLAAKM-----------------------EEIL--VPSLFDFQVA---------------GVKYLFEAKTIKRMELLVLSVLDWRLR", ) self.assertEqual( alignment[81], "DRIKEMLVREI--EFCPGTDYVKRLLSGD---LDL-SVRNQALDW---ILKVCAHYHFGHLCICLSMNYLDRFLT-SY-ELPKDK---DWAAQLLAVSCLSLASKM-----------------------EETD--VPHIVDLQVE---------------DPKFVFEAKTIKRMELLVVTTLNWRLQ", ) self.assertEqual( alignment[82], "EIIMEMVEKEK--QHLPSDDYIKRLRSGD---LDLNVGRRDALNW---IWKACEVHQFGPLCFCLAMNYLDRFLS-VH-DLPSGK---GWILQLLAVACLSLAAKI-----------------------EETE--VPMLIDLQVG---------------DPQFVFEAKSVQRMELLVLNKLKWRLR", ) self.assertEqual( alignment[83], "EELTSLFSKET--EYEISYNVLEK----N---QSFISSRRESVEW---ILKTTAYYSFSAQTGFLAVNYFDRFLL--F-SFNQSLNHKPWMNQLVAVTCLSLAAKV-----------------------EETD--VPLLLDLQVE---------------ESGFLFESKTIQRMEMLILSTLKWKMN", ) self.assertEqual( alignment[84], "DELATLLSKEN--EFHLGFQSLIS----D---GSLMGARKEALDW---MLRVIAYYGFTATTAVLAVNYFDRFVS-GW-CFQKDK---PWMSQLAAVACLSIAAKV-----------------------EETQ--VPLLLDLQVA---------------DSRFVFEAKTIQRMELLVLSTLKWKMN", ) self.assertEqual( alignment[85], "DELSTLISKQE--------PCLYDEILDD---EFLVLCREKALDW---IFKVKSHYGFNSLTALLAVNYFDRFIT-SR-KFQTDK---PWMSQLTALACLSLAAKV-----------------------EEIR--VPFLLDFQVE---------------EARYVFEAKTIQRMELLVLSTLDWRMH", ) self.assertEqual( alignment[86], "TLPHSLFLVEF--QHMPSSHYFHSLKSSA---FLL-SNRNQAISS---ITQYSRKFD-DPSLTYLAVNYLDRFLS-SE-DMPQSK---PWILKLISLSCVSLSAKM-----------------------RKPD---MSVSDLPVE---------------GE--FFDAQMIERMENVILGALKWRMR", ) self.assertEqual( alignment[87], "DVWRLMCHRDEQDSRLRSISML--EQHPG---LQP-RMRAILLDW---LIEVCEVYKLHRETFYLAVDYLDRYLHVAH-KVQKT------HLQLIGITCLFVAAKV-----------------------EEIY--PPKIGEFAYVT--------------DG--ACTERDILNHEKILLQALDWDIS", ) self.assertEqual( alignment[88], "EVWQNMLQKEN--RYVHDKHFQ--VLHSD---LEP-QMRSILLDW---LLEVCEVYTLHRETFYLAQDFFDRFMLTQK-DVNKN------MLQLIGITSLFIASKL-----------------------EEIY--APKLQEFAYVT--------------DG--ACSEVDILKMELNILKALKWELC", ) self.assertEqual( alignment[89], "DVWKNMINKEE--TYVRDKLYM--QRHPL---LQP-KMRTILLDW---LMEVCEVYKLYRETFYLAQDFFDRFMATQQ-NVVKT------LLQLIGISSLFIAAKL-----------------------EEIY--PPKLHQFAYVT--------------DG--ACTEDEILSMELIIMKALNWNLN", ) self.assertEqual( alignment[90], "EVWRIMLNKEK--TYLRDEHFL--QRHPL---LQA-RMRAVLLDW---LMEVCEVYKLHRETFYLAQDFFDRYMASQH-NIIKT------LLQLIGISALFIASKL-----------------------EEIY--PPKLHQFAYVT--------------DG--ACSGDEILTMELMMMKALKWRLS", ) self.assertEqual( alignment[91], "EVWNNLLGKDK--LYLRDTRVM--ERHPN---LQP-KMRAILLDW---LMEVCEVYKLHRETFYLGQDYFDRFMATQE-NVLKT------TLQLIGISCLFIAAKM-----------------------EEIY--PPKVHQFAYVT--------------DG--ACTEDDILSMEIIIMKELNWSLS", ) self.assertEqual( alignment[92], "DVWRNMLNKDR--TYLRDKNFF--QKHPQ---LQP-NMRAILLDW---LMEVCEVYKLHRETFYLGQDFFDRFMATQK-NVIKS------RLQLIGITSLFIAAKL-----------------------EEIY--PPKLHQFAFIT--------------DG--ACTEDEITSMELIIMKDLDWCLS", ) self.assertEqual( alignment[93], "EVWTIMTRKEA--LCPRKHDCL--KSHPS---LGE-RMRAILLDW---LIEVCEVYRLHRESFYLAADFVDRYLAAKE-NVPKT------KLQLIGITSLFVAAKL-----------------------EEIY--PPKLHEFAYVT--------------DG--ACTDDQILDQELIMLMTLNWDLT", ) self.assertEqual( alignment[94], "KVWSLMVKRDE--IPRATRFLL--GNHPD---MDD-EKRRILIDW---MMEVCESEKLHRETFHLAVDYVDRYLESSNVECSTD------NFQLVGTAALFIAAKY-----------------------EEIY--PPKCIDFAHLT--------------DS--AFTCDNIRTMEVLIVKYIGWSLG", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], "HHHHHHHHHHC..HTS-STTCT.TTCTSS...S-H.HHHHHHHHH...HHHHHHHTT--TTHHHHHHHHHHHHHH.HS.---CC......CHHHHHHHHHHHHHHH.......................HSSS..---HHHHHHHT..............TT..SS-HHHHHHHHHHHHHHTTT---", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "-IapahpptEt..phhsp.sYh..ppps-...ls..pMRsILlDW...Ll-VppcacLhtETLaLulshlDRFLu.tp.sls+s......cLQLlGlsulhlAuKa.......................EElh..sPplp-hshlo..............Ds..saopcpllpMEphlLpsLpasls", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[0, 1, 2, 4, 11, 11, 11, 11, 12, 13, 14, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 11, 12, 13, 14, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 11, 12, 13, 14, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 11, 12, 13, 14, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 20, 20, 20, 21, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 20, 20, 20, 21, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 15, 16, 18, 19, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 30, 31, 33, 34, 35, 39, 39, 48, 49, 66, 66, 67, 68, 68, 73, 73, 73, 73, 73, 89, 89, 89, 89, 92, 93, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 28, 30, 31, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 68, 69, 69, 74, 74, 74, 74, 74, 90, 90, 90, 90, 93, 94, 94, 95, 96, 97, 104, 105, 105, 105, 105, 105, 105, 105, 105, 107, 107, 109, 110, 127, 128, 130], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 28, 30, 31, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 68, 69, 69, 74, 74, 74, 74, 74, 90, 90, 90, 90, 93, 94, 94, 95, 96, 97, 104, 105, 105, 105, 105, 105, 105, 105, 105, 107, 107, 109, 110, 127, 128, 130], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 90, 91, 92, 93, 100, 101, 101, 101, 101, 101, 101, 101, 101, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 11, 11, 12, 13, 14, 15, 17, 18, 18, 18, 20, 21, 22, 23, 23, 25, 26, 26, 27, 29, 30, 31, 35, 35, 44, 45, 62, 62, 63, 64, 64, 69, 69, 69, 69, 69, 85, 86, 86, 87, 90, 91, 91, 91, 91, 92, 99, 100, 100, 100, 100, 100, 100, 100, 100, 102, 102, 104, 105, 122, 123, 125], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 22, 23, 25, 26, 27, 28, 28, 30, 31, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 68, 69, 69, 74, 74, 74, 74, 74, 90, 90, 90, 90, 93, 94, 94, 95, 96, 97, 104, 105, 105, 105, 105, 105, 105, 105, 105, 107, 107, 109, 110, 127, 128, 130], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 124, 126], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 89, 110, 111, 114, 115, 115, 116, 117, 118, 125, 126, 126, 126, 126, 126, 126, 126, 126, 128, 130, 132, 133, 150, 151, 153], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 11, 11, 11, 12, 13, 14, 15, 16, 18, 19, 19, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 0, 1, 3, 10, 10, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 25, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 102, 102, 102, 102, 102, 102, 102, 102, 104, 104, 106, 107, 124, 125, 127], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 22, 23, 25, 26, 27, 28, 28, 30, 31, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 68, 69, 69, 74, 74, 74, 74, 74, 90, 90, 90, 90, 93, 94, 94, 95, 96, 97, 104, 105, 105, 105, 105, 105, 105, 105, 105, 107, 107, 109, 110, 127, 128, 130], [0, 0, 0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 19, 19, 19, 21, 22, 23, 24, 24, 26, 27, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 90, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 21, 23, 24, 25, 26, 26, 28, 29, 29, 30, 32, 33, 34, 38, 38, 47, 48, 65, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 14, 15, 16, 19, 21, 22, 23, 24, 26, 27, 28, 32, 32, 41, 42, 59, 59, 60, 61, 61, 66, 66, 66, 66, 66, 82, 82, 82, 82, 85, 86, 88, 89, 90, 91, 98, 99, 99, 99, 99, 99, 99, 99, 99, 101, 101, 103, 104, 121, 122, 124], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 29, 29, 29, 29, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 90, 90, 91, 92, 93, 100, 101, 103, 103, 103, 103, 103, 103, 105, 107, 109, 111, 112, 129, 130, 132], [0, 0, 0, 0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 22, 23, 24, 25, 28, 30, 31, 32, 33, 35, 36, 37, 41, 44, 53, 54, 71, 71, 72, 73, 73, 78, 78, 78, 78, 78, 94, 94, 94, 94, 97, 97, 97, 98, 99, 100, 107, 108, 110, 111, 111, 111, 111, 112, 114, 116, 118, 120, 121, 138, 139, 141], [0, 1, 2, 4, 11, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 28, 28, 28, 28, 28, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 70, 70, 70, 70, 86, 86, 86, 86, 89, 89, 89, 90, 91, 92, 99, 100, 102, 103, 104, 104, 105, 106, 108, 110, 112, 114, 115, 132, 133, 135], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 29, 29, 29, 29, 29, 31, 32, 33, 37, 37, 46, 47, 64, 64, 65, 66, 66, 71, 71, 71, 71, 71, 87, 87, 87, 87, 90, 90, 90, 91, 92, 93, 100, 101, 103, 104, 105, 111, 112, 113, 115, 117, 119, 121, 122, 139, 140, 142], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 29, 29, 29, 29, 29, 29, 29, 30, 34, 34, 43, 44, 61, 61, 61, 61, 61, 66, 67, 67, 67, 68, 84, 84, 84, 84, 87, 88, 88, 89, 90, 91, 98, 99, 101, 102, 103, 109, 110, 111, 113, 115, 117, 119, 119, 136, 137, 139], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 67, 67, 67, 72, 73, 76, 77, 78, 94, 94, 94, 94, 97, 98, 98, 99, 100, 101, 108, 109, 109, 109, 109, 109, 109, 109, 109, 111, 111, 113, 114, 131, 132, 134], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 29, 29, 29, 29, 29, 29, 30, 31, 35, 35, 44, 45, 62, 62, 62, 62, 62, 67, 68, 71, 72, 73, 89, 89, 89, 89, 92, 93, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 28, 28, 28, 28, 28, 28, 28, 29, 30, 34, 34, 43, 44, 61, 61, 61, 61, 61, 66, 67, 70, 71, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 29, 29, 29, 29, 29, 29, 30, 31, 35, 35, 44, 45, 62, 62, 63, 64, 65, 70, 71, 71, 71, 72, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 95, 96, 98, 99, 99, 99, 100, 101, 103, 103, 103, 105, 106, 123, 124, 126], [0, 1, 2, 4, 4, 4, 4, 4, 4, 4, 5, 6, 7, 9, 10, 11, 12, 14, 15, 16, 17, 20, 22, 23, 24, 25, 27, 28, 28, 32, 32, 41, 42, 59, 60, 61, 62, 63, 68, 68, 68, 68, 68, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 91, 92, 94, 95, 96, 96, 97, 98, 100, 100, 100, 102, 103, 120, 121, 123], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 30, 31, 33, 34, 35, 39, 39, 48, 49, 66, 66, 67, 68, 68, 73, 74, 74, 75, 76, 92, 92, 92, 92, 95, 96, 96, 97, 98, 99, 106, 106, 106, 106, 106, 106, 106, 106, 106, 108, 110, 112, 113, 130, 131, 133], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 30, 31, 33, 34, 35, 39, 39, 48, 49, 66, 66, 67, 68, 68, 73, 74, 74, 75, 76, 92, 92, 92, 92, 95, 96, 96, 97, 98, 99, 106, 106, 106, 106, 106, 106, 106, 106, 106, 108, 110, 112, 113, 130, 131, 133], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 31, 32, 34, 35, 36, 40, 40, 49, 50, 67, 67, 68, 69, 69, 74, 75, 75, 76, 77, 93, 93, 93, 93, 96, 97, 97, 98, 99, 100, 107, 107, 107, 107, 107, 107, 107, 107, 107, 109, 111, 113, 114, 131, 132, 134], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 22, 22, 22, 23, 23, 25, 26, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 63, 64, 64, 69, 70, 73, 74, 75, 91, 91, 91, 91, 94, 95, 95, 96, 97, 98, 105, 105, 105, 105, 105, 105, 105, 105, 105, 107, 109, 111, 112, 129, 130, 132], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 22, 22, 22, 23, 23, 25, 26, 27, 28, 30, 31, 32, 36, 36, 45, 46, 63, 63, 64, 65, 65, 70, 71, 71, 72, 73, 89, 89, 89, 89, 92, 93, 93, 94, 95, 96, 103, 103, 103, 103, 103, 103, 103, 103, 103, 105, 107, 109, 110, 127, 128, 130], [0, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 14, 15, 16, 18, 19, 20, 21, 21, 23, 24, 25, 26, 28, 29, 30, 34, 34, 43, 44, 61, 61, 62, 63, 63, 68, 69, 69, 70, 71, 87, 87, 87, 87, 90, 91, 91, 92, 93, 94, 101, 101, 101, 101, 101, 101, 101, 101, 101, 103, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 25, 26, 27, 27, 29, 30, 30, 31, 33, 34, 35, 39, 39, 48, 48, 65, 65, 66, 67, 67, 72, 73, 73, 74, 75, 91, 91, 91, 91, 94, 95, 95, 95, 96, 97, 104, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], [0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 22, 22, 24, 25, 26, 27, 27, 29, 30, 30, 31, 33, 34, 35, 39, 39, 48, 49, 66, 67, 68, 69, 69, 74, 74, 74, 74, 74, 90, 90, 90, 90, 93, 94, 94, 95, 96, 97, 104, 105, 105, 105, 105, 105, 105, 105, 105, 107, 107, 109, 110, 127, 128, 130], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 67, 72, 72, 72, 72, 72, 88, 88, 88, 88, 91, 92, 92, 93, 94, 95, 102, 103, 103, 103, 103, 103, 103, 103, 103, 105, 105, 107, 108, 125, 126, 128], [0, 1, 2, 4, 11, 11, 11, 12, 13, 14, 15, 16, 17, 19, 20, 20, 20, 22, 23, 24, 25, 25, 27, 28, 28, 29, 31, 32, 33, 37, 37, 46, 47, 64, 65, 66, 67, 68, 73, 73, 73, 73, 73, 89, 89, 89, 89, 92, 93, 93, 94, 95, 96, 103, 104, 104, 104, 104, 104, 104, 104, 104, 106, 106, 108, 109, 126, 127, 129], ] # fmt: on ), ) ) self.assertEqual( str(alignment), """\ CCNB3_CAE 0 GIFDYYRHREV---HFRVRKYL--HKHPE---VDV-KTRAILIDW---MVEIQETFELNH T1FNQ9_HE 0 DIFDYYRDREV---KFRIPDYM--FQQTD---LTP-SMRAILVDW---LVEVQQSFELNH CCNB3_DRO 0 DIFNYLKVREA---EFPIADYM--PRQIH---LTT-WMRTLLVDW---MVEVQETFELNH CCNB3_CHI 0 EIFDYMREREE---KFLLPDYM--EKQSD---ISR-DMRAILVDW---MVEVQENFELNH CCB31_ARA 0 DIYQFYWTAEA--LNPALGHYL--SAHAE---VSP-VTRGILINW---LIEVHFKFDLMH CCNB1_SOY 0 DIYKFYKLVEN--ESRP-HDYI--GSQPE---INE-RMRAILVDW---LIDVHTKFELSL CCB11_ARA 0 DIYSFYKSVES--EWRP-RDYM--ASQPD---INE-KMRLILVEW---LIDVHVRFELNP CCB12_ARA 0 DMYSFYKEVEK--ESQP-KMYM--HIQTE---MNE-KMRAILIDW---LLEVHIKFELNL M1A5P4_SO 0 DIYKFYKLTED--ENRP-CDYM--DSQPE---IND-RVRAILVDW---LIEAHKRFELRP I1M770_SO 0 DIYKFYKETEE--DGCV-HDYM--GSQPD---INA-KMRSILVDW---LIEVHRKFELMP CCB14_ARA 0 DIFKFYRTVEE--EGGI-KDYI--GSQPE---INE-KMRSILIDW---LVDVHRKFELMP B8A2G9_MA 0 DIYRFYKSTEG--TCLPLSSYM--SSQAE---ISE-RMRAILIDW---IIEVQYRLTLMP B4FZZ7_MA 0 DIYTFYKIAQH--DRRP-CDYI--DTQVE---INP-KMRAILAGW---IIEVHHKFELMP K7V0X7_MA 0 DIYTFYKTAQH--ESRP-IDYM--GNQPE---LSP-RMRSILADW---LIESHRRFQLMP CCB21_ORY 0 ELYKFYRENEE--MSCVQPDYM--SSQGD---INE-KMRAILIDW---LIEVHHKFELMD CCB21_ARA 0 DLYAFYRTMER--FSCVPVDYM--MQQID---LNE-KMRAILIDW---LIEVHDKFDLIN Q9XGI1_SO 0 DLFANYRTMEV--NSCASPYYM--AQQAD---INE-RMRSILIDW---LIEVHHKFELRE C4J9B6_MA 0 EIYRFYRKTEG--ASCVPTNYM--SSQTD---INE-KMRGILIDW---LIEVHYKLELLE CCB24_ARA 0 DIYCFYKKNEC--RSCVPPNYM--ENQHD---INE-RMRGILFDW---LIEVHYKFELME CCNB_DICD 0 EIFAYYREKEQ--IDKIDKDYI--KNQYH---INE-RMRAILVDW---MMAVHVRFKLLS O45926_CA 0 DIYNYLVHHEK--KYVLDDSFI------NGGNVNS-KMRRILVDW---LIQVHLRFHLTP CCNB1_CAE 0 DIYKYLVHHEK--KYLLEECFM------EGGEPTP-KMRRILVDW---LVQVHVRFHLTP P92162_BO 0 DIYKYLTELEE--KYSIEPDHL--KKQTV---ITG-KMRATLIDW---LVEVQRQFSLVL CCNB_DROM 0 DIYDYLYQVEL--EQPIHKDHL--AGQKE---VSH-KMRAVLIDW---INEVHLQFHLAA F6QF79_XE 0 DIYCYLRSLEN--AQAVRQNYL--HG-QE---VTG-NMRAILIDW---LVQVQMKFRLLQ CCNB1_MOU 0 DIYAYLRQLEE--EQSVRPKYL--QG-RE---VTG-NMRAILIDW---LIQVQMKFRLLQ Q28HA1_XE 0 DIYNYLKQLEV--QQSVRPCYL--EG-KE---INE-RMRAILVDW---IVQVHSRFQLLQ CCNB2_HUM 0 DIYQYLRQLEV--LQSINPHFL--DG-RD---ING-RMRAILVDW---LVQVHSKFRLLQ CCNB2_CHI 0 DIYLYLRQLEL--QQSVRPHYL--DG-KT---ING-RMRAILVDW---LVQVHSRFQLLQ A0BXX7_PA 0 EILQHLLIEEN--KYTI-NQYMTPEQQPD---INI-KMRAILVDW---LIDVHAKFKLKD Q6BFS2_PA 0 EIYTYLLTQEE--KYLVSNNYMNEQQQPD---LNA-RMRAILLDW---LIDVHLKFKLRD CG21_CANA 0 EIFSYYYELET--RMLPDPQYL--FKQTL---LKP-RMRSILVDW---LVEMHLKFKLLP CGS5_YEAS 0 EIFAFLYRREL--ETLPSHNYL--LDKTSKYYLRP-SMRTILVDW---LVEVHEKFQCYP CGS6_YEAS 0 SIFSHLYEKEI--QMLPTHNYL--MDTQSPYHLKS-SMRALLIDW---LVEVHEKFHCLP CG21_YEAS 0 DIFDYLHHLEI--ITLPNKANL--YKHKN---IK--QNRDILVNW---IIKIHNKFGLLP CG22_YEAS 0 DIFEYLHQLEV--ITLPKKEDL--YQHRN---IH--QNRDILVNW---LVKIHNKFGLLP CG24_CANA 0 EIFNYLHELEN--KFTPDPNYM--DFQDD---LKW-EMRAVLIDW---VVQVHARFNLFS CG23_YEAS 0 EIFEYMRKLED--LYKPNPYYM--DKQPE---LRW-SFRSTLIDW---IVQVHEKFQLLP CG24_YEAS 0 DIFYYLRELEV--KYRPNPYYM--QNQVE---LTW-PFRRTMIDW---LVQLHFRFQLLP CG22_SCHP 0 EIFEYIRKLDL--KCLPNPKYM--DQQKE---LTW-KMREILNEW---LVEIHSNFCLMP M7PCR8_PN 0 EIMSYMRELEV--LTLPLPDYM--DRQKE---LQW-KMRGILVDW---LIEVHAKFRLLP CG21_EMEN 0 EIFDYLRELEM--ETLPNPDYI--DHQPD---LEW-KMRGILVDW---LIEVHTRFRLLP CG23_SCHP 0 DIFEYLNELEI--ETMPSPTYM--DRQKE---LAW-KMRGILTDW---LIEVHSRFRLLP CG21_SCHP 0 EIFHYMQSLER--KLAPPPNYM--SVQQE---IDW-VTRHMLVDW---IVQVQIHFRLLP REM1_SCHP 0 EILSHMEKLEI--RFMPDYRHM--SAQPY---YVT-EMRASVINW---IVGVHTCINLLP CCNF_MOUS 0 SVCQLFQASQA----VNKQQIF--SVQKG---LSD-TMRYILIDW---LVEVATMKDFTS I1K835_SO 0 DIHGYLREMEMQNKRRPMVDYI-EKVQKI---VTP-TMRAILVDW---LVEVAVEYKLLS J3KY10_OR 0 DIYMHLREAET--RKRPSTDFM-ETIQKD---VNP-SMRAILIDW---LVEVAEEYRLVP M4E4A3_BR 0 DIYNHLRAAEA--KKQPAVDYM-ATVQKD---VNS-TMRGILVDW---LVEVSEEYRLVP CCA22_ARA 0 DIYDNIHVAEL--QQRPLANYM-ELVQRD---IDP-DMRKILIDW---LVEVSDDYKLVP Q39878_SO 0 DIYSNIRVTEL--QRKPLTNYM-DKLQKD---INP-SMRGILVDW---LVEVSEEYKLVP T1EGC7_HE 0 DILTYGKEAEQ--RYMAKANYM--ERQSD---INH-SMRSILVDW---LVEVADEYKLKR CCNA1_CAE 0 DIIKYMLHRQT--KNRASHECF--DIQSQ---VNE-EMRTILIDW---FSDVVKEYNFQK CCNA_DROM 0 DILEYFRESEK--KHRPKPLYM--RRQKD---ISH-NMRSILIDW---LVEVSEEYKLDT W4XJF2_ST 0 EIYQYLKTAES--KHRPKHGYM--RKQPD---ITN-SMRCILVDW---LVEVSEEYRLHN CCNA2_MOU 0 DIHTYLREMEV--KCKPKVGYM--KRQPD---ITN-SMRAILVDW---LVEVGEEYKLQN E9QJ66_DA 0 DIHRYLRECEV--KYRPKPGYM--RKQPD---ITN-CMRVILVDW---LVEVGEEYKLCS CCNA1_HUM 0 EIYQYLREAEI--RHRPKAHYM--KKQPD---ITE-GMRTILVDW---LVEVGEEYKLRA CG12_YEAS 0 EISTNVIAQSC--KFKPNPKLI--DQQPE---MNPVETRSNIITF---LFELSVVTRVTN PUC1_SCHP 0 DIIHHLITREK--NFLLNVHLS--NQQPE---LRW-SMRPALVNF---IVEIHNGFDLSI CG13_CANA 0 EMLHHLLSVEA--KTLPNLSLI--EQQPE---IKL-GMRPLLLDF---LMEVITILSLSR CG11_CANA 0 DIVNTLSQLES--LTLVNPAMI--DLQPE---IQW-FMRPFLLDF---LIELHSSFKLQP CGH2_SHV2 0 RVLNNLKLREL---LLPKFTSL-WEIQTE---VTV-DNRTILLTW---MHLLCESFELDK VCYCL_HHV 0 -IFYNILEIEP--RFLTSDSVFGTFQQS----LTS-HMRKLLGTW---MFSVCQEYNLEP CCND_CAEE 0 DMRAFYNCMEYEEALQPNYHYF-TGVQEN---ITP-FHREQAIDW---IYDVAKEENCDG Q7KUZ5_DR 0 --LENFLKVEEKHHKIPDTYF---SIQKD---ITP-PMRKIVAEW---MMEVCAEENCQE CCND1_RAT 0 RVLRAMLKTEE--TCAPSVSYF-KCVQRE---IVP-SMRKIVATW---MLEVCEEQKCEE CCND2_MOU 0 RVLQNLLTIEE--RYLPQCSYF-KCVQKD---IQP-YMRRMVATW---MLEVCEEQKCEE CCND3_HUM 0 RVLQSLLRLEE--RYVPRASYF-QCVQRE---IKP-HMRKMLAYW---MLEVCEEQRCEE Q9VZP3_DR 0 DIFLTMREQEL-------------SRRPLFYLSPQLNERRRMLQL---LKLATSAHKLSR SSN8_YEAS 0 DSKQNGIEQSITKNIPITHRDLHYDKDYN--------LRIYCYFL---IMKLGRRLNIRQ CCC11_ORY 0 ----NFWTSSHCKQLLDQEDVDKVPQADSDRGITLEEFRLVKIHMSFHIWRLAQQVKVRQ CCNT_DROM 0 DKIWYFSNDQL-ANSPSRRCGIKGDDELQ--------YRQMTAYL---IQEMGQRLQVSQ CCT12_ARA 0 IIPWFFSREEIERNSPSRRDGIDLKTETR--------LRDSYCTF---LEILGERLKVPQ Q9VE72_DR 0 DVMSMQQHVELNKAQTMKPIDYRKMNKPG-----------VVPMY---IFECAAKLKMKP PCL1_YEAS 0 DIIKFLTDTTL--RVVPSSNYPTPPGSPG---EKHLTRLPSLMTF---ITRLVRYTNVYT PCL2_YEAS 0 EMVQYLASTTASIIKIKKTNSMIDIALPA----------PPLTKF---INRLIKHSNVQT PCL9_YEAS 0 EMIQFLATSTASIIKIRENNNPIQGCRP-----------PDLSIF---IKNVVIQSNVQT CCU41_ARA 0 RVAESNDLTRRVATQSQRVSVFHGLSRPT----------ITIQSY---LERIFKYANCSP Q9VKF0_DR 0 DIFD------------EKLHPLTHDQVPDNYDTHNPEHRQ-IYKF---VRTLFNAAQLTA CCD11_ARA 0 DSIACFIEDER--HFVPGHDYLSRFQTRS---LDA-SAREDSVAW---ILKVQAYYNFQP CCD21_ARA 0 DRIKEMLVREI--EFCPGTDYVKRLLSGD---LDL-SVRNQALDW---ILKVCAHYHFGH CCD41_ARA 0 EIIMEMVEKEK--QHLPSDDYIKRLRSGD---LDLNVGRRDALNW---IWKACEVHQFGP Q9SMD4_SO 0 EELTSLFSKET--EYEISYNVLEK----N---QSFISSRRESVEW---ILKTTAYYSFSA Q9S7H9_SO 0 DELATLLSKEN--EFHLGFQSLIS----D---GSLMGARKEALDW---MLRVIAYYGFTA CCD33_ARA 0 DELSTLISKQE--------PCLYDEILDD---EFLVLCREKALDW---IFKVKSHYGFNS CCD61_ARA 0 TLPHSLFLVEF--QHMPSSHYFHSLKSSA---FLL-SNRNQAISS---ITQYSRKFD-DP CCNE_DROM 0 DVWRLMCHRDEQDSRLRSISML--EQHPG---LQP-RMRAILLDW---LIEVCEVYKLHR CCNE2_MOU 0 EVWQNMLQKEN--RYVHDKHFQ--VLHSD---LEP-QMRSILLDW---LLEVCEVYTLHR CCNE1_CHI 0 DVWKNMINKEE--TYVRDKLYM--QRHPL---LQP-KMRTILLDW---LMEVCEVYKLYR CCNE1_MOU 0 EVWRIMLNKEK--TYLRDEHFL--QRHPL---LQA-RMRAVLLDW---LMEVCEVYKLHR A0A0R4IZF 0 EVWNNLLGKDK--LYLRDTRVM--ERHPN---LQP-KMRAILLDW---LMEVCEVYKLHR F6QUN0_XE 0 DVWRNMLNKDR--TYLRDKNFF--QKHPQ---LQP-NMRAILLDW---LMEVCEVYKLHR W4XEA0_ST 0 EVWTIMTRKEA--LCPRKHDCL--KSHPS---LGE-RMRAILLDW---LIEVCEVYRLHR CCNE_CAEE 0 KVWSLMVKRDE--IPRATRFLL--GNHPD---MDD-EKRRILIDW---MMEVCESEKLHR CCNB3_CAE 48 ETLYNAVKLTDMYLCKTK-NVDKN------TIQKLACVAIFIAAKY-------------- T1FNQ9_HE 48 ETLYMAVKLIDIFSS-KV-TIKRN------KLQLIGAVALNLACKF-------------- CCNB3_DRO 48 ETLYLAVKIVDLYLC-RE-VINKE------KLQLLGAAAFFIACKY-------------- CCNB3_CHI 48 ETLYLAVKLVDHYLV-EV-VSMRD------KLQLIGSTAVLIASKF-------------- CCB31_ARA 49 ETLYLTMDLLDRYLS-QV-PIHKN------EMQLIGLTALLLASKY-------------- CCNB1_SOY 48 ETLYLTINIIDRFLA-VK-TVPRR------ELQLVGISAMLMASKY-------------- CCB11_ARA 48 ETFYLTVNILDRFLS-VK-PVPRK------ELQLVGLSALLMSAKY-------------- CCB12_ARA 48 ETLYLTVNIIDRFLS-VK-AVPKR------ELQLVGISALLIASKY-------------- M1A5P4_SO 48 ESLYLTVNIMDRFLS-EE-TVPRR------ELQLLCISSMLIACKY-------------- I1M770_SO 48 ETLYLTLNIVDRFLS-VK-AVPRR------ELQLVGISSMLIASKY-------------- CCB14_ARA 48 ETLYLTINLVDRFLS-LT-MVHRR------ELQLLGLGAMLIACKY-------------- B8A2G9_MA 49 ETLYLTVYIIDQYLS-ME-SVPRK------ELQLVGISAMLIASKY-------------- B4FZZ7_MA 48 ETLYLTMYIIDQYLS-LQ-PVLRR------ELQLVGVSAMLIACKY-------------- K7V0X7_MA 48 ETLYLTIYIVDRYLS-LQ-PTPRR------ELQLVGVAALLIACKY-------------- CCB21_ORY 49 ETLFLTVNIVDRFLE-KQ-VVPRK------KLQLVGVTAMLLACKY-------------- CCB21_ARA 49 ETLFLTVNLIDRFLS-KQ-NVMRK------KLQLVGLVALLLACKY-------------- Q9XGI1_SO 49 ETLFLTVNLIDRFLE-KQ-GIVRK------KLQLVGLVAMLLACKY-------------- C4J9B6_MA 49 ETLFLTVNIIDRFLA-RE-NVVRK------KLQLAGVTAMLLACKY-------------- CCB24_ARA 49 ETLYLTINLIDRFLAVHQ-HIARK------KLQLVGVTAMLLACKY-------------- CCNB_DICD 49 ETFFLSVNIVDRYLA-KV-MIPVT------KLQLVGITAILLACKY-------------- O45926_CA 48 ETLHLTIFVLDRIIV-KN-IVSKA------EFQLLGVAALFVASKF-------------- CCNB1_CAE 48 ETLHLTVFILDRMLQ-KK-VTSKA------DLQLLGISAMFVASKF-------------- P92162_BO 49 ETFHLTVGIIDRYLQVVP-NVQRN------QLQLVGVTAMFIASKY-------------- CCNB_DROM 49 ETFQLAVAIIDRYLQVVK-DTKRT------YLQLVGVTALFIATKY-------------- F6QF79_XE 48 ETMFMTVGIIDRFLQ-DH-PVPKN------QLQLVGVTAMFLAAKY-------------- CCNB1_MOU 48 ETMYMTVSIIDRFMQ-NS-CVPKK------MLQLVGVTAMFIASKY-------------- Q28HA1_XE 48 ETLYMGIAIMDRFLQ-VQ-PVSRS------KLQLVGVTSLLVASKY-------------- CCNB2_HUM 48 ETLYMCVGIMDRFLQ-VQ-PVSRK------KLQLVGITALLLASKY-------------- CCNB2_CHI 48 ETLYMCVAVMDRFLQ-SH-PVPRK------RLQLVGVTALLLASKY-------------- A0BXX7_PA 50 ETLYITISLIDRYLA-LA-QVTRM------RLQLVGVAALFIACKY-------------- Q6BFS2_PA 51 ETLYVTTYLIDRFLN-FK-TTTRQ------QLQLVGVASLFIACKY-------------- CG21_CANA 49 ESLFLAVNVMDRFMS-VE-VVQID------KLQLLATAALFTAAKY-------------- CGS5_YEAS 52 ETLFLSINLMDRFLA-KN-KVTMN------KLQLLAVTSLFIAAKF-------------- CGS6_YEAS 52 ETLFLAINLLDRFLS-QN-VVKLN------KLQLLCITCLFIACKF-------------- CG21_YEAS 48 ETLYLAINIMDRFLC-EE-VVQLN------RLQLVGTSCLFIASKY-------------- CG22_YEAS 48 ETLYLAINIMDRFLG-KE-LVQLD------KLQLVGTSCLFIASKY-------------- CG24_CANA 49 ETLYLTVNYIDRFLS-KR-RVSLS------RFQLVGAVALFIAAKY-------------- CG23_YEAS 49 ETLYLCINIIDRYLC-KE-VVPVN------KFQLVGAASLFIAAKY-------------- CG24_YEAS 49 ETLYLTINIVDRFLS-KK-TVTLN------RFQLVGVSALFIAAKF-------------- CG22_SCHP 49 ETLYLAVNIIDRFLS-RR-SCSLS------KFQLTGITALLIASKY-------------- M7PCR8_PN 49 ETLFLSVNIIDRFLS-LR-VCSLP------KLQLVGITALFIAAKY-------------- CG21_EMEN 49 ETLFLAVNIIDRFLS-AE-VVALD------RLQLVGVAAMFIASKY-------------- CG23_SCHP 49 ETLFLAVNIIDRFLS-LR-VCSLN------KLQLVGIAALFIASKY-------------- CG21_SCHP 49 ETLFLAVNLIDRFLS-IK-VVSLQ------KVQLVGLSALLIACKY-------------- REM1_SCHP 49 ESLFLSINVLDRFLS-LQ-NVPAS------KMKLCGATALFIACKY-------------- CCNF_MOUS 47 LCLHLTVECVDRYLR-RR-LVPRY------KLQLLGIACMVICTRFI------------- I1K835_SO 52 DTLHLSVSYIDRFLS-VN-PVSKS------RLQLLGVSSMLIAAKY-------------- J3KY10_OR 50 DTLYLTVNYIDRYLS-GN-EINRQ------RLQLLGVACMLIAAKY-------------- M4E4A3_BR 50 ETLYLTVNYIDRYLS-GN-VISRQ------KLQLLGVACMMIAAKY-------------- CCA22_ARA 50 DTLYLTVNLIDRFLS-NS-YIERQ------RLQLLGVSCMLIASKY-------------- Q39878_SO 50 DTLYLTVNLIDRYLS-TR-LIQKQ------KLQLLGVTCMLIASKY-------------- T1EGC7_HE 49 ETFFLAVNYIDRFLS-MM-SVIRC------RLQLLGAAAMFIAAKY-------------- CCNA1_CAE 49 ETFHLAVSLVDRALS-MF-NIDKM------RFQLVGTTSMMIAVKY-------------- CCNA_DROM 49 ETLYLSVFYLDRFLS-QM-AVVRS------KLQLVGTAAMYIAAKY-------------- W4XJF2_ST 49 ETLYLAAAFIDRFLS-QM-SVLRA------KLQLVGTASMFVASKY-------------- CCNA2_MOU 49 ETLHLAVNYIDRFLS-SM-SVLRG------KLQLVGTAAMLLASKF-------------- E9QJ66_DA 49 ETLYLAVNYLDRFLS-CM-SVLRG------KLQLVGTAAILLAAKY-------------- CCNA1_HUM 49 ETLYLAVNFLDRFLS-CM-SVLRG------KLQLVGTAAMLLASKY-------------- CG12_YEAS 50 GIFFHSVRLYDRYCS-KR-IVLRD------QAKLVVATCLWLAAKTWGGCNHIINNVVIP PUC1_SCHP 49 DTLPLSISLMDSYVS-RR-VVYCK------HIQLVACVCLWIASKF-------------- CG13_CANA 49 STFPLTVNLIDRYCS-TR-IVKKQ------HYQLLGLTSLWISCKN-------------- CG11_CANA 49 TTLFLCLNIIDRYCA-KR-IVFKR------HYQLVGCTALWIASKY-------------- CGH2_SHV2 49 SVFPLSVSILDRYLC-KK-QGTKK------TLQKIGAACVLIGSKI-------------- VCYCL_HHV 49 NVVALALNLLDRLLL-IK-QVSKE------HFQKTGSACLLVASKL-------------- CCND_CAEE 52 DVFLLAVSLIDRFMS-VQ-NILKH------DIQMIAGVALFIASKL-------------- Q7KUZ5_DR 48 EVVLLALNYMDRFLS-SK-SVRKT------QLQILAAACLLLASKL-------------- CCND1_RAT 50 EVFPLAMNYLDRFLS-LE-PLKKS------RLQLLGATCMFVASKM-------------- CCND2_MOU 50 EVFPLAMNYLDRFLA-GV-PTPKT------HLQLLGAVCMFLASKL-------------- CCND3_HUM 50 EVFPLAMNYLDRYLS-CV-PTRKA------QLQLLGAVCMLLASKL-------------- Q9VZP3_DR 44 CALHLAVYYMDRFVD-YY-KIRPD------KLLLVAITCLHIAAQI-------------- SSN8_YEAS 49 YALATAHIYLSRFLI-KA-SVREI------NLYMLVTTCVYLACKV-------------- CCC11_ORY 56 RVIATAVTYFRRVYT-RK-SMTEY------DPRLVAPTCLYLASKV-------------- CCNT_DROM 48 LCINTAIVYMHRFYA-FH-SFTHF------HRNSMASASLFLAAKV-------------- CCT12_ARA 49 VTIATAIFFCHRFFL-RQ-SHAKN------DRQTIATVCMLLAGKV-------------- Q9VE72_DR 46 LTAACAAIVFHRFFR----EVKASD----YDEFLIAAGSLYLAGKI-------------- PCL1_YEAS 52 PTLLTAACYLNKLKR----ILPRDATGLPSTIHRIFLACLILSAKF-------------- PCL2_YEAS 47 PTLMATSVYLAKLRS----IIPSNVYGIETTRHRIFLGCLILAAKT-------------- PCL9_YEAS 46 PTLMATSVYLNKLKS----VIPKNVYGINTTRHRIFLGCLILAAKT-------------- CCU41_ARA 47 SCFVVAYVYLDRFTH-RQPSLPINS----FNVHRLLITSVMVAAKF-------------- Q9VKF0_DR 44 ECAIITLVYLERLLTYAELDVGPC------NWKRMVLGAILLASKV-------------- CCD11_ARA 51 LTAYLAVNYMDRFLY-AR-RLPETS---GWPMQLLAVACLSLAAKM-------------- CCD21_ARA 51 LCICLSMNYLDRFLT-SY-ELPKDK---DWAAQLLAVSCLSLASKM-------------- CCD41_ARA 52 LCFCLAMNYLDRFLS-VH-DLPSGK---GWILQLLAVACLSLAAKI-------------- Q9SMD4_SO 48 QTGFLAVNYFDRFLL--F-SFNQSLNHKPWMNQLVAVTCLSLAAKV-------------- Q9S7H9_SO 48 TTAVLAVNYFDRFVS-GW-CFQKDK---PWMSQLAAVACLSIAAKV-------------- CCD33_ARA 46 LTALLAVNYFDRFIT-SR-KFQTDK---PWMSQLTALACLSLAAKV-------------- CCD61_ARA 50 SLTYLAVNYLDRFLS-SE-DMPQSK---PWILKLISLSCVSLSAKM-------------- CCNE_DROM 51 ETFYLAVDYLDRYLHVAH-KVQKT------HLQLIGITCLFVAAKV-------------- CCNE2_MOU 49 ETFYLAQDFFDRFMLTQK-DVNKN------MLQLIGITSLFIASKL-------------- CCNE1_CHI 49 ETFYLAQDFFDRFMATQQ-NVVKT------LLQLIGISSLFIAAKL-------------- CCNE1_MOU 49 ETFYLAQDFFDRYMASQH-NIIKT------LLQLIGISALFIASKL-------------- A0A0R4IZF 49 ETFYLGQDYFDRFMATQE-NVLKT------TLQLIGISCLFIAAKM-------------- F6QUN0_XE 49 ETFYLGQDFFDRFMATQK-NVIKS------RLQLIGITSLFIAAKL-------------- W4XEA0_ST 49 ESFYLAADFVDRYLAAKE-NVPKT------KLQLIGITSLFVAAKL-------------- CCNE_CAEE 49 ETFHLAVDYVDRYLESSNVECSTD------NFQLVGTAALFIAAKY-------------- CCNB3_CAE 87 ---------DERS--PPLVDDLIYLS--------------GD--RFSRDELLAMERELFA T1FNQ9_HE 86 ---------EERC--PPMLDDFVYVC--------------DD--AYPRQEFLKMEELVFQ CCNB3_DRO 86 ---------DERQ--PPLIEDFLYIC--------------DG--AYNHDELVRMERETLR CCNB3_CHI 86 ---------EERC--PPCVDDFLYIC--------------DD--AYKREELIAMETSILR CCB31_ARA 87 ---------EDYW--HPRIKDLISIS--------------AE--SYTREQILGMERSMLK CCNB1_SOY 86 ---------EEIW--PPEVNDFVCLS--------------DR--AYTHEHILTMEKTILN CCB11_ARA 86 ---------EEIW--PPQVEDLVDIA--------------DH--AYSHKQILVMEKTILS CCB12_ARA 86 ---------EEIW--PPQVNDLVYVT--------------DN--AYSSRQILVMEKAILG M1A5P4_SO 86 ---------EEIW--APEVNDFLTIT--------------DN--AYVRDQILLMEKVILG I1M770_SO 86 ---------EEIW--APEVNDFVCIS--------------DN--AYVSEQVLMMEKTILR CCB14_ARA 86 ---------EEIW--APEVNDFVCIS--------------DN--AYNRKQVLAMEKSILG B8A2G9_MA 87 ---------EEIW--APLVKDLMCLC--------------DN--AFTRDQILTKEKAILD B4FZZ7_MA 86 ---------EEIW--APEVNDFILIS--------------DS--AYSREQILSMEKGILN K7V0X7_MA 86 ---------EEIW--APEVNDLIHIA--------------DG--AFNRSQILAAEKAILN CCB21_ORY 87 ---------EEVA--VPVVEDLVLIS--------------DR--AYTKGQILEMEKLILN CCB21_ARA 87 ---------EEVS--VPVVEDLVLIS--------------DK--AYTRNDVLEMEKTMLS Q9XGI1_SO 87 ---------EEVC--APLVEDLVLIS--------------DK--AYTRKEVLEMESMMLN C4J9B6_MA 87 ---------EEVS--VPVVEDLILIC--------------DR--AYTRADILEMERRIVN CCB24_ARA 88 ---------EEVS--VPVVDDLILIS--------------DK--AYTRTEILDMEKLMAN CCNB_DICD 87 ---------EEIY--SPQIKDFVHTS--------------DD--ACTHAEVIDMERQILS O45926_CA 86 ---------EDIY--LPDILEYEMIT--------------DN--TFSKKQIMAMEQTILN CCNB1_CAE 86 ---------EEVY--LPDIHDYEFIT--------------EN--TYSKKQILAMEQTILN P92162_BO 88 ---------EEIY--APDVGDFVYVT--------------DN--AYTKSDVFRCERDIMC CCNB_DROM 88 ---------EELF--PPAIGDFVFIT--------------DD--TYTARQIRQMELQIFK F6QF79_XE 86 ---------EEMY--PPEIGDFTFVT--------------DH--TYTKAQIRDMEMKVLR CCNB1_MOU 86 ---------EEMY--PPEIGDFAFVT--------------NN--TYTKHQIRQMEMKILR Q28HA1_XE 86 ---------EEMY--TPEVADFVYIT--------------DN--AYTASQIREMEMIILR CCNB2_HUM 86 ---------EEMF--SPNIEDFVYIT--------------DN--AYTSSQIREMETLILK CCNB2_CHI 86 ---------EEMY--SPDIADFVYIT--------------DN--AYNSAEVREMEITILK A0BXX7_PA 88 ---------EEIY--PPALKDFVYIT--------------DN--AYVKSDVLEMEGLMLQ Q6BFS2_PA 89 ---------EEIY--PPDLKDFVYIT--------------DN--AYTKQDVLEMEGQILQ CG21_CANA 87 ---------EEVF--SPSVKNYAYFT--------------DG--SYTPEEVVQAEKYMLT CGS5_YEAS 90 ---------EEVN--LPKLAEYAYIT--------------DG--AASKNDIKNAEMFMLT CGS6_YEAS 90 ---------EEVK--LPKITNFAYVT--------------DG--AATVEGIRKAELFVLS CG21_YEAS 86 ---------EEIY--SPSIKHFAYET--------------DG--ACSVEDIKEGERFILE CG22_YEAS 86 ---------EEVY--SPSIKHFASET--------------DG--ACTEDEIKEGEKFILK CG24_CANA 87 ---------EEIN--CPTVQEIAYMA--------------DN--AYSIDEFLKAERFMID CG23_YEAS 87 ---------EEIN--CPTIKDFVYMS--------------EN--CYSRNDLLDAERTILN CG24_YEAS 87 ---------EEIN--CPTLDDLVYML--------------EN--TYTRDDIIRAEQYMID CG22_SCHP 87 ---------EEVM--CPSIQNFVYMT--------------DG--AFTVEDVCVAERYMLN M7PCR8_PN 87 ---------EEVM--CPSIQNFMYMA--------------DG--GYTNEEILKAEQYVLQ CG21_EMEN 87 ---------EEVL--SPHVANFSHVA--------------DE--TFSDKEILDAERHILA CG23_SCHP 87 ---------EEVM--CPSVQNFVYMA--------------DG--GYDEEEILQAERYILR CG21_SCHP 87 ---------EEIH--PPSIYNFAHVV--------------QG--IFTVDEIIRAERYMLM REM1_SCHP 87 ---------EEIH--PPTVKDLEIVL--------------EG--EWIGEDICGMEKYMLM CCNF_MOUS 86 --------SKEIL----TIREAVWLT--------------DN--TYKYEDLVRVMGEIIS I1K835_SO 90 ---------EEMD--PPGVDEFCSIT--------------DH--TYDKTEVVKMEADILK J3KY10_OR 88 ---------EEIC--APQVEEFCYIT--------------DN--TYFRDEVLEMEASVLN M4E4A3_BR 88 ---------EEVC--APQVEEFCYIT--------------DN--TYLKDEVLDMESAVLN CCA22_ARA 88 ---------EELS--APGVEEFCFIT--------------AN--TYTRPEVLSMEIQILN Q39878_SO 88 ---------EEMC--APRVEEFCFIT--------------DN--TYTKEEVLKMEREVLN T1EGC7_HE 87 ---------EEIY--PPDVAEFVYIT--------------DD--TYTMKQVLQMEQAILK CCNA1_CAE 87 ---------EEIF--PPEIEDFALIT--------------DN--TYRVPDILLMERFLLG CCNA_DROM 87 ---------EEIY--PPEVGEFVFLT--------------DD--SYTKAQVLRMEQVILK W4XJF2_ST 87 ---------EEIY--PPDVKEFVYIT--------------DD--TYSIKQVLRMEHLILK CCNA2_MOU 87 ---------EEIY--PPEVAEFVYIT--------------DD--TYSKKQVLRMEHLVLK E9QJ66_DA 87 ---------EEVY--PPEVDEFVYIT--------------DD--TYTKKQLLRMEQHLLR CCNA1_HUM 87 ---------EEIY--PPEVDEFVYIT--------------DD--TYTKRQLLKMEHLLLK CG12_YEAS 102 TGGRFYGPNPRAR--IPRLSELVHYC--------------GDGQVFDESMFLQMERHILD PUC1_SCHP 87 ---------HETEDRVPLLQELKLAC--------------KN--IYAEDLFIRMERHILD CG13_CANA 87 ---------LDSKFKVPTLNDLRKIC--------------VD--SYYKELFVEMEKHILK CG11_CANA 87 ---------EDKKSRVPTLKELTIMC--------------RN--AYDEEMFVQMEMHILS CGH2_SHV2 87 ---------RTVK--PMTVSKLTYLS--------------CD--CFTNLELINQEKDILE VCYCL_HHV 87 ---------RSLT--PISTSSLCYAA--------------AD--SFSRQELIDQEKELLE CCND_CAEE 90 ---------KAPH--PMTASKIAYYS--------------DN--SCPIDMILQWELLIVT Q7KUZ5_DR 86 ---------REPSCRALSVDLLVVYT--------------DN--SIYKDDLIKWELYVLS CCND1_RAT 88 ---------KETI--PLTAEKLCIYT--------------DN--SIRPEELLQMELLLVN CCND2_MOU 88 ---------KETI--PLTAEKLCIYT--------------DN--SVKPQELLEWELVVLG CCND3_HUM 88 ---------RETT--PLTIEKLCIYT--------------DH--AVSPRQLRDWEVLVLG Q9VZP3_DR 82 ---------ENTDAFIPRYSEMNRLV--------------KN--AYTAFEYKAVERKILC SSN8_YEAS 87 ---------EEC---PQYIRTLVSEART----------LWPEFIPPDPTKVTEFEFYLLE CCC11_ORY 94 ---------EES---TVQARLLVFYIKKM--------CASDEKYRFEIKDILEMEMKLLE CCNT_DROM 86 ---------EEQ---PRKLEHVIRAANKCL------PPTTEQNYAELAQELVFNENVLLQ CCT12_ARA 87 ---------EET---PVTLEDVIIASYERIHKKDLAGAQRKEVYDQQKELVLIGEELVLS Q9VE72_DR 84 ---------KEDE--SVKIRDVINVAYCTLNRGNDPVDLNDEYWSM-RDAIVQAELLITR PCL1_YEAS 94 ---------HNDS--SPLNKHWARYT--------------DG--LFTLEDINLMERQLLQ PCL2_YEAS 89 ---------LNDS--SPLNKHWAEYT--------------DG--LLILREVNTIERELLE PCL9_YEAS 88 ---------LNDS--SPWNKHWTTYT--------------EG--LLRIREVNTIERELLE CCU41_ARA 88 ------------------LDDLYYNNAYY-------AKVG----GISTKEMNFLELDFLF Q9VKF0_DR 84 ------------------WDDQAVWNVDYC------QILK----DITVEDMNELERQFLE CCD11_ARA 92 ---------EEIL--VPSLFDFQVA---------------GVKYLFEAKTIKRMELLVLS CCD21_ARA 92 ---------EETD--VPHIVDLQVE---------------DPKFVFEAKTIKRMELLVVT CCD41_ARA 93 ---------EETE--VPMLIDLQVG---------------DPQFVFEAKSVQRMELLVLN Q9SMD4_SO 91 ---------EETD--VPLLLDLQVE---------------ESGFLFESKTIQRMEMLILS Q9S7H9_SO 89 ---------EETQ--VPLLLDLQVA---------------DSRFVFEAKTIQRMELLVLS CCD33_ARA 87 ---------EEIR--VPFLLDFQVE---------------EARYVFEAKTIQRMELLVLS CCD61_ARA 91 ---------RKPD---MSVSDLPVE---------------GE--FFDAQMIERMENVILG CCNE_DROM 90 ---------EEIY--PPKIGEFAYVT--------------DG--ACTERDILNHEKILLQ CCNE2_MOU 88 ---------EEIY--APKLQEFAYVT--------------DG--ACSEVDILKMELNILK CCNE1_CHI 88 ---------EEIY--PPKLHQFAYVT--------------DG--ACTEDEILSMELIIMK CCNE1_MOU 88 ---------EEIY--PPKLHQFAYVT--------------DG--ACSGDEILTMELMMMK A0A0R4IZF 88 ---------EEIY--PPKVHQFAYVT--------------DG--ACTEDDILSMEIIIMK F6QUN0_XE 88 ---------EEIY--PPKLHQFAFIT--------------DG--ACTEDEITSMELIIMK W4XEA0_ST 88 ---------EEIY--PPKLHEFAYVT--------------DG--ACTDDQILDQELIMLM CCNE_CAEE 89 ---------EEIY--PPKCIDFAHLT--------------DS--AFTCDNIRTMEVLIVK CCNB3_CAE 120 TVGYDLG 127 T1FNQ9_HE 119 AVGFDIG 126 CCNB3_DRO 119 VIKYDLG 126 CCNB3_CHI 119 TLNFDIN 126 CCB31_ARA 120 QLKFRLN 127 CCNB1_SOY 119 KLEWTLT 126 CCB11_ARA 119 TLEWYLT 126 CCB12_ARA 119 NLEWYLT 126 M1A5P4_SO 119 KLEWYLT 126 I1M770_SO 119 KLEWYLT 126 CCB14_ARA 119 QVEWYIT 126 B8A2G9_MA 120 MLHWNLT 127 B4FZZ7_MA 119 SLEWNLT 126 K7V0X7_MA 119 SMEWNLT 126 CCB21_ORY 120 TLQFNMS 127 CCB21_ARA 120 TLQFNIS 127 Q9XGI1_SO 120 TLQFNMS 127 C4J9B6_MA 120 TLNFNMS 127 CCB24_ARA 121 TLQFNFC 128 CCNB_DICD 120 TLQFHMS 127 O45926_CA 119 ALNFDLS 126 CCNB1_CAE 119 SLNFDLS 126 P92162_BO 121 KLGFCLA 128 CCNB_DROM 121 AIDCNLS 128 F6QF79_XE 119 VLKFAIG 126 CCNB1_MOU 119 VLNFSLG 126 Q28HA1_XE 119 VLNFDLG 126 CCNB2_HUM 119 ELKFELG 126 CCNB2_CHI 119 ELNFDLG 126 A0BXX7_PA 121 ALNFNIC 128 Q6BFS2_PA 122 TLDFSIT 129 CG21_CANA 120 ILNFDLN 127 CGS5_YEAS 123 SLEFNIG 130 CGS6_YEAS 123 SLGYNIS 130 CG21_YEAS 119 KLDFQIS 126 CG22_YEAS 119 TLKFNLN 126 CG24_CANA 120 VLEFDLG 127 CG23_YEAS 120 GLEFELG 127 CG24_YEAS 120 TLEFEIG 127 CG22_SCHP 120 VLNFDLS 127 M7PCR8_PN 120 VLGYDMS 127 CG21_EMEN 120 TLEYNMS 127 CG23_SCHP 120 VLEFNLA 127 CG21_SCHP 120 LLDFDIS 127 REM1_SCHP 120 VLQYQLG 127 CCNF_MOUS 118 ALEGKIR 125 I1K835_SO 123 SLKFEMG 130 J3KY10_OR 121 YLKFEMT 128 M4E4A3_BR 121 YLKFEMS 128 CCA22_ARA 121 FVHFRLS 128 Q39878_SO 121 LVHFQLS 128 T1EGC7_HE 120 TLNF-LV 126 CCNA1_CAE 120 KFDFVVA 127 CCNA_DROM 120 ILSFDLC 127 W4XJF2_ST 120 VLSFDLA 127 CCNA2_MOU 120 VLAFDLA 127 E9QJ66_DA 120 VLAFDMT 127 CCNA1_HUM 120 VLAFDLT 127 CG12_YEAS 146 TLNWNIY 153 PUC1_SCHP 122 TLDWDIS 129 CG13_CANA 122 SLEWVVN 129 CG11_CANA 122 TLDWSIG 129 CGH2_SHV2 120 ALKWDTE 127 VCYCL_HHV 120 KLAWRTE 127 CCND_CAEE 123 TLQWETE 130 Q7KUZ5_DR 121 RLGWDLS 128 CCND1_RAT 121 KLKWNLA 128 CCND2_MOU 121 KLKWNLA 128 CCND3_HUM 121 KLKWDLA 128 Q9VZP3_DR 117 FLNFELI 124 SSN8_YEAS 125 ELESYLI 132 CCC11_ORY 134 ALDYYLV 141 CCNT_DROM 128 TLGFDVA 135 CCT12_ARA 135 TLNFDLC 142 Q9VE72_DR 132 TLCFDLN 139 PCL1_YEAS 127 LLNWDLR 134 PCL2_YEAS 122 YFDWDVT 129 PCL9_YEAS 121 YLNWDVR 128 CCU41_ARA 119 GLGFELN 126 Q9VKF0_DR 116 LLQFNIN 123 CCD11_ARA 126 VLDWRLR 133 CCD21_ARA 126 TLNWRLQ 133 CCD41_ARA 127 KLKWRLR 134 Q9SMD4_SO 125 TLKWKMN 132 Q9S7H9_SO 123 TLKWKMN 130 CCD33_ARA 121 TLDWRMH 128 CCD61_ARA 122 ALKWRMR 129 CCNE_DROM 123 ALDWDIS 130 CCNE2_MOU 121 ALKWELC 128 CCNE1_CHI 121 ALNWNLN 128 CCNE1_MOU 121 ALKWRLS 128 A0A0R4IZF 121 ELNWSLS 128 F6QUN0_XE 121 DLDWCLS 128 W4XEA0_ST 121 TLNWDLT 128 CCNE_CAEE 122 YIGWSLG 129 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID Cyclin_N #=GF AC PF00134.25 #=GF DE Cyclin, N-terminal domain #=GF AU Bateman A;0000-0002-6982-4660 #=GF AU Sonnhammer ELL;0000-0002-9015-5588 #=GF AU Griffiths-Jones SR;0000-0001-6043-807X #=GF SE Prosite #=GF GA 20.50 20.50; #=GF TC 20.50 20.50; #=GF NC 20.40 20.40; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF PI cyclin; #=GF CL CL0065 #=GF WK Cyclin #=GF RC The cyclins include an internal duplication, which is related to that #=GF RC found in TFIIB and the RB protein. #=GF RN [1] #=GF RM 8152925 #=GF RT Evidence for a protein domain superfamily shared by the cyclins, #=GF RT TFIIB and RB/p107. #=GF RA Gibson TJ, Thompson JD, Blocker A, Kouzarides T; #=GF RL Nucleic Acids Res 1994;22:946-952. #=GF RN [2] #=GF RM 8591034 #=GF RT The crystal structure of cyclin A #=GF RA Brown NR, Noble MEM, Endicott JA, Garman EF, Wakatsuki S, Mitchell E, Rasmussen B, Hunt T, Johnson LN; #=GF RL Structure. 1995;3:1235-1247. #=GF RC Complex of cyclin and cyclin dependent kinase. #=GF RN [3] #=GF RM 8756328 #=GF RT Structural basis of cyclin-dependant kinase activation by #=GF RT phosphorylation. #=GF RA Russo AA, Jeffrey PD, Pavletich NP; #=GF RL Nat Struct Biol. 1996;3:696-700. #=GF RN [4] #=GF RM 2001396 #=GF RT Isolation and characterization of a human cDNA encoding uracil-DNA #=GF RT glycosylase. #=GF RA Muller SJ, Caradonna S; #=GF RL Biochim Biophys Acta 1991;1088:197-207. #=GF DR INTERPRO; IPR006671; #=GF DR PROSITE; PDOC00264; #=GF DR SCOP; 1vin; fa; #=GF DR HOMSTRAD; cyclin; #=GF DR SO; 0000417; polypeptide_domain; #=GF CC Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a #=GF CC Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins #=GF CC contain two domains of similar all-alpha fold, of which this family #=GF CC corresponds with the N-terminal domain. #=GF SQ 95 #=GS CCNB3_CAEEL/115-241 AC Q10654.3 #=GS T1FNQ9_HELRO/256-381 AC T1FNQ9.1 #=GS CCNB3_DROME/308-433 AC Q9I7I0.1 #=GS CCNB3_CHICK/149-274 AC P39963.1 #=GS CCB31_ARATH/146-272 AC Q9SA32.2 #=GS CCNB1_SOYBN/197-322 AC P25011.1 #=GS CCB11_ARATH/168-293 AC P30183.2 #=GS CCB12_ARATH/185-310 AC Q39067.2 #=GS M1A5P4_SOLTU/185-310 AC M1A5P4.1 #=GS I1M770_SOYBN/186-311 AC I1M770.1 #=GS CCB14_ARATH/133-258 AC O48790.1 #=GS B8A2G9_MAIZE/228-354 AC B8A2G9.1 #=GS B4FZZ7_MAIZE/193-318 AC B4FZZ7.1 #=GS K7V0X7_MAIZE/191-316 AC K7V0X7.1 #=GS CCB21_ORYSJ/157-283 AC Q7XSJ6.2 #=GS CCB21_ARATH/174-300 AC Q39068.2 #=GS Q9XGI1_SOLLC/180-306 AC Q9XGI1.1 #=GS C4J9B6_MAIZE/173-299 AC C4J9B6.1 #=GS CCB24_ARATH/180-307 AC Q9SFW6.2 #=GS CCNB_DICDI/188-314 AC P42524.1 #=GS O45926_CAEEL/34-159 AC O45926.2 #=GS CCNB1_CAEEL/81-206 AC Q10653.1 #=GS P92162_BOMMO/260-387 AC P92162.1 #=GS CCNB_DROME/260-387 AC P20439.2 #=GS F6QF79_XENTR/139-264 AC F6QF79.3 #=GS CCNB1_MOUSE/170-295 AC P24860.3 #=GS Q28HA1_XENTR/132-257 AC Q28HA1.1 #=GS CCNB2_HUMAN/137-262 AC O95067.1 #=GS CCNB2_CHICK/141-266 AC P29332.1 #=GS A0BXX7_PARTE/85-212 AC A0BXX7.1 #=GS Q6BFS2_PARTE/82-210 AC Q6BFS2.1 #=GS CG21_CANAL/208-334 AC Q5ALY0.1 #=GS CGS5_YEAST/165-294 AC P30283.1 #=GS CGS6_YEAST/123-252 AC P32943.2 #=GS CG21_YEAST/212-337 AC P24868.1 #=GS CG22_YEAST/232-357 AC P24869.1 #=GS CG24_CANAL/234-360 AC Q5A0A9.1 #=GS CG23_YEAST/171-297 AC P24870.3 #=GS CG24_YEAST/210-336 AC P24871.2 #=GS CG22_SCHPO/139-265 AC P36630.2 #=GS M7PCR8_PNEMU/176-302 AC M7PCR8.1 #=GS CG21_EMENI/211-337 AC P30284.1 #=GS CG23_SCHPO/206-332 AC P10815.1 #=GS CG21_SCHPO/166-292 AC P24865.2 #=GS REM1_SCHPO/145-271 AC O14332.1 #=GS CCNF_MOUSE/282-406 AC P51944.2 #=GS I1K835_SOYBN/85-214 AC I1K835.1 #=GS J3KY10_ORYBR/200-327 AC J3KY10.1 #=GS M4E4A3_BRARP/154-281 AC M4E4A3.1 #=GS CCA22_ARATH/175-302 AC Q147G5.1 #=GS Q39878_SOYBN/207-334 AC Q39878.1 #=GS T1EGC7_HELRO/166-291 AC T1EGC7.1 #=GS CCNA1_CAEEL/215-341 AC P34638.2 #=GS CCNA_DROME/206-332 AC P14785.3 #=GS W4XJF2_STRPU/207-333 AC W4XJF2.1 #=GS CCNA2_MOUSE/171-297 AC P51943.2 #=GS CCNA2_MOUSE/171-297 DR PDB; 4I3Z D; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 4II5 D; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 4I3Z B; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 4II5 B; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 3QHW B; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 3QHW D; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 3QHR D; 181-307; #=GS CCNA2_MOUSE/171-297 DR PDB; 3QHR B; 181-307; #=GS E9QJ66_DANRE/140-266 AC E9QJ66.1 #=GS CCNA1_HUMAN/214-340 AC P78396.1 #=GS CG12_YEAST/43-195 AC P20438.2 #=GS PUC1_SCHPO/99-227 AC P25009.1 #=GS CG13_CANAL/44-172 AC Q5A1N6.1 #=GS CG11_CANAL/44-172 AC Q59YH3.2 #=GS CGH2_SHV21/22-148 AC Q01043.1 #=GS CGH2_SHV21/22-148 DR PDB; 1JOW A; 22-148; #=GS CGH2_SHV21/22-148 DR PDB; 1BU2 A; 22-148; #=GS CGH2_SHV21/22-148 DR PDB; 2EUF A; 22-148; #=GS CGH2_SHV21/22-148 DR PDB; 4TTH A; 22-148; #=GS CGH2_SHV21/22-148 DR PDB; 1XO2 A; 22-148; #=GS CGH2_SHV21/22-148 DR PDB; 2F2C A; 22-148; #=GS VCYCL_HHV8P/21-147 AC Q77Q36.1 #=GS CCND_CAEEL/72-201 AC Q9U2M5.1 #=GS Q7KUZ5_DROME/153-280 AC Q7KUZ5.1 #=GS CCND1_RAT/26-153 AC P39948.1 #=GS CCND2_MOUSE/24-151 AC P30280.1 #=GS CCND3_HUMAN/26-153 AC P30281.2 #=GS CCND3_HUMAN/26-153 DR PDB; 3G33 D; 26-153; #=GS CCND3_HUMAN/26-153 DR PDB; 3G33 B; 26-153; #=GS Q9VZP3_DROME/42-165 AC Q9VZP3.1 #=GS SSN8_YEAST/45-176 AC P47821.1 #=GS CCC11_ORYSJ/4-144 AC P93411.1 #=GS CCNT_DROME/42-176 AC O96433.2 #=GS CCT12_ARATH/28-169 AC Q56YF8.2 #=GS Q9VE72_DROME/6-144 AC Q9VE72.1 #=GS PCL1_YEAST/19-152 AC P24867.1 #=GS PCL2_YEAST/18-146 AC P25693.2 #=GS PCL9_YEAST/19-146 AC Q12477.1 #=GS CCU41_ARATH/23-148 AC O80513.1 #=GS Q9VKF0_DROME/205-327 AC Q9VKF0.1 #=GS CCD11_ARATH/50-182 AC P42751.3 #=GS CCD21_ARATH/65-197 AC P42752.3 #=GS CCD41_ARATH/45-178 AC Q8LGA1.2 #=GS Q9SMD4_SOLLC/51-182 AC Q9SMD4.1 #=GS Q9S7H9_SOLLC/61-190 AC Q9S7H9.1 #=GS CCD33_ARATH/59-186 AC Q9SN11.1 #=GS CCD61_ARATH/26-154 AC Q9ZR04.1 #=GS CCNE_DROME/330-459 AC P54733.2 #=GS CCNE2_MOUSE/112-239 AC Q9Z238.1 #=GS CCNE1_CHICK/112-239 AC P49707.1 #=GS CCNE1_MOUSE/113-240 AC Q61457.2 #=GS A0A0R4IZF8_DANRE/117-244 AC A0A0R4IZF8.1 #=GS F6QUN0_XENTR/114-241 AC F6QUN0.2 #=GS W4XEA0_STRPU/126-253 AC W4XEA0.1 #=GS CCNE_CAEEL/232-360 AC O01501.2 CCNB3_CAEEL/115-241 GIFDYYRHREV...HFRVRKYL..HKHPE...VDV.KTRAILIDW...MVEIQETFELNHETLYNAVKLTDMYLCKTK.NVDKN......TIQKLACVAIFIAAKY.......................DERS..PPLVDDLIYLS..............GD..RFSRDELLAMERELFATVGYDLG T1FNQ9_HELRO/256-381 DIFDYYRDREV...KFRIPDYM..FQQTD...LTP.SMRAILVDW...LVEVQQSFELNHETLYMAVKLIDIFSS.KV.TIKRN......KLQLIGAVALNLACKF.......................EERC..PPMLDDFVYVC..............DD..AYPRQEFLKMEELVFQAVGFDIG CCNB3_DROME/308-433 DIFNYLKVREA...EFPIADYM..PRQIH...LTT.WMRTLLVDW...MVEVQETFELNHETLYLAVKIVDLYLC.RE.VINKE......KLQLLGAAAFFIACKY.......................DERQ..PPLIEDFLYIC..............DG..AYNHDELVRMERETLRVIKYDLG CCNB3_CHICK/149-274 EIFDYMREREE...KFLLPDYM..EKQSD...ISR.DMRAILVDW...MVEVQENFELNHETLYLAVKLVDHYLV.EV.VSMRD......KLQLIGSTAVLIASKF.......................EERC..PPCVDDFLYIC..............DD..AYKREELIAMETSILRTLNFDIN CCB31_ARATH/146-272 DIYQFYWTAEA..LNPALGHYL..SAHAE...VSP.VTRGILINW...LIEVHFKFDLMHETLYLTMDLLDRYLS.QV.PIHKN......EMQLIGLTALLLASKY.......................EDYW..HPRIKDLISIS..............AE..SYTREQILGMERSMLKQLKFRLN CCNB1_SOYBN/197-322 DIYKFYKLVEN..ESRP.HDYI..GSQPE...INE.RMRAILVDW...LIDVHTKFELSLETLYLTINIIDRFLA.VK.TVPRR......ELQLVGISAMLMASKY.......................EEIW..PPEVNDFVCLS..............DR..AYTHEHILTMEKTILNKLEWTLT CCB11_ARATH/168-293 DIYSFYKSVES..EWRP.RDYM..ASQPD...INE.KMRLILVEW...LIDVHVRFELNPETFYLTVNILDRFLS.VK.PVPRK......ELQLVGLSALLMSAKY.......................EEIW..PPQVEDLVDIA..............DH..AYSHKQILVMEKTILSTLEWYLT CCB12_ARATH/185-310 DMYSFYKEVEK..ESQP.KMYM..HIQTE...MNE.KMRAILIDW...LLEVHIKFELNLETLYLTVNIIDRFLS.VK.AVPKR......ELQLVGISALLIASKY.......................EEIW..PPQVNDLVYVT..............DN..AYSSRQILVMEKAILGNLEWYLT M1A5P4_SOLTU/185-310 DIYKFYKLTED..ENRP.CDYM..DSQPE...IND.RVRAILVDW...LIEAHKRFELRPESLYLTVNIMDRFLS.EE.TVPRR......ELQLLCISSMLIACKY.......................EEIW..APEVNDFLTIT..............DN..AYVRDQILLMEKVILGKLEWYLT I1M770_SOYBN/186-311 DIYKFYKETEE..DGCV.HDYM..GSQPD...INA.KMRSILVDW...LIEVHRKFELMPETLYLTLNIVDRFLS.VK.AVPRR......ELQLVGISSMLIASKY.......................EEIW..APEVNDFVCIS..............DN..AYVSEQVLMMEKTILRKLEWYLT CCB14_ARATH/133-258 DIFKFYRTVEE..EGGI.KDYI..GSQPE...INE.KMRSILIDW...LVDVHRKFELMPETLYLTINLVDRFLS.LT.MVHRR......ELQLLGLGAMLIACKY.......................EEIW..APEVNDFVCIS..............DN..AYNRKQVLAMEKSILGQVEWYIT B8A2G9_MAIZE/228-354 DIYRFYKSTEG..TCLPLSSYM..SSQAE...ISE.RMRAILIDW...IIEVQYRLTLMPETLYLTVYIIDQYLS.ME.SVPRK......ELQLVGISAMLIASKY.......................EEIW..APLVKDLMCLC..............DN..AFTRDQILTKEKAILDMLHWNLT B4FZZ7_MAIZE/193-318 DIYTFYKIAQH..DRRP.CDYI..DTQVE...INP.KMRAILAGW...IIEVHHKFELMPETLYLTMYIIDQYLS.LQ.PVLRR......ELQLVGVSAMLIACKY.......................EEIW..APEVNDFILIS..............DS..AYSREQILSMEKGILNSLEWNLT K7V0X7_MAIZE/191-316 DIYTFYKTAQH..ESRP.IDYM..GNQPE...LSP.RMRSILADW...LIESHRRFQLMPETLYLTIYIVDRYLS.LQ.PTPRR......ELQLVGVAALLIACKY.......................EEIW..APEVNDLIHIA..............DG..AFNRSQILAAEKAILNSMEWNLT CCB21_ORYSJ/157-283 ELYKFYRENEE..MSCVQPDYM..SSQGD...INE.KMRAILIDW...LIEVHHKFELMDETLFLTVNIVDRFLE.KQ.VVPRK......KLQLVGVTAMLLACKY.......................EEVA..VPVVEDLVLIS..............DR..AYTKGQILEMEKLILNTLQFNMS CCB21_ARATH/174-300 DLYAFYRTMER..FSCVPVDYM..MQQID...LNE.KMRAILIDW...LIEVHDKFDLINETLFLTVNLIDRFLS.KQ.NVMRK......KLQLVGLVALLLACKY.......................EEVS..VPVVEDLVLIS..............DK..AYTRNDVLEMEKTMLSTLQFNIS Q9XGI1_SOLLC/180-306 DLFANYRTMEV..NSCASPYYM..AQQAD...INE.RMRSILIDW...LIEVHHKFELREETLFLTVNLIDRFLE.KQ.GIVRK......KLQLVGLVAMLLACKY.......................EEVC..APLVEDLVLIS..............DK..AYTRKEVLEMESMMLNTLQFNMS C4J9B6_MAIZE/173-299 EIYRFYRKTEG..ASCVPTNYM..SSQTD...INE.KMRGILIDW...LIEVHYKLELLEETLFLTVNIIDRFLA.RE.NVVRK......KLQLAGVTAMLLACKY.......................EEVS..VPVVEDLILIC..............DR..AYTRADILEMERRIVNTLNFNMS CCB24_ARATH/180-307 DIYCFYKKNEC..RSCVPPNYM..ENQHD...INE.RMRGILFDW...LIEVHYKFELMEETLYLTINLIDRFLAVHQ.HIARK......KLQLVGVTAMLLACKY.......................EEVS..VPVVDDLILIS..............DK..AYTRTEILDMEKLMANTLQFNFC CCNB_DICDI/188-314 EIFAYYREKEQ..IDKIDKDYI..KNQYH...INE.RMRAILVDW...MMAVHVRFKLLSETFFLSVNIVDRYLA.KV.MIPVT......KLQLVGITAILLACKY.......................EEIY..SPQIKDFVHTS..............DD..ACTHAEVIDMERQILSTLQFHMS O45926_CAEEL/34-159 DIYNYLVHHEK..KYVLDDSFI......NGGNVNS.KMRRILVDW...LIQVHLRFHLTPETLHLTIFVLDRIIV.KN.IVSKA......EFQLLGVAALFVASKF.......................EDIY..LPDILEYEMIT..............DN..TFSKKQIMAMEQTILNALNFDLS CCNB1_CAEEL/81-206 DIYKYLVHHEK..KYLLEECFM......EGGEPTP.KMRRILVDW...LVQVHVRFHLTPETLHLTVFILDRMLQ.KK.VTSKA......DLQLLGISAMFVASKF.......................EEVY..LPDIHDYEFIT..............EN..TYSKKQILAMEQTILNSLNFDLS P92162_BOMMO/260-387 DIYKYLTELEE..KYSIEPDHL..KKQTV...ITG.KMRATLIDW...LVEVQRQFSLVLETFHLTVGIIDRYLQVVP.NVQRN......QLQLVGVTAMFIASKY.......................EEIY..APDVGDFVYVT..............DN..AYTKSDVFRCERDIMCKLGFCLA CCNB_DROME/260-387 DIYDYLYQVEL..EQPIHKDHL..AGQKE...VSH.KMRAVLIDW...INEVHLQFHLAAETFQLAVAIIDRYLQVVK.DTKRT......YLQLVGVTALFIATKY.......................EELF..PPAIGDFVFIT..............DD..TYTARQIRQMELQIFKAIDCNLS F6QF79_XENTR/139-264 DIYCYLRSLEN..AQAVRQNYL..HG.QE...VTG.NMRAILIDW...LVQVQMKFRLLQETMFMTVGIIDRFLQ.DH.PVPKN......QLQLVGVTAMFLAAKY.......................EEMY..PPEIGDFTFVT..............DH..TYTKAQIRDMEMKVLRVLKFAIG CCNB1_MOUSE/170-295 DIYAYLRQLEE..EQSVRPKYL..QG.RE...VTG.NMRAILIDW...LIQVQMKFRLLQETMYMTVSIIDRFMQ.NS.CVPKK......MLQLVGVTAMFIASKY.......................EEMY..PPEIGDFAFVT..............NN..TYTKHQIRQMEMKILRVLNFSLG Q28HA1_XENTR/132-257 DIYNYLKQLEV..QQSVRPCYL..EG.KE...INE.RMRAILVDW...IVQVHSRFQLLQETLYMGIAIMDRFLQ.VQ.PVSRS......KLQLVGVTSLLVASKY.......................EEMY..TPEVADFVYIT..............DN..AYTASQIREMEMIILRVLNFDLG CCNB2_HUMAN/137-262 DIYQYLRQLEV..LQSINPHFL..DG.RD...ING.RMRAILVDW...LVQVHSKFRLLQETLYMCVGIMDRFLQ.VQ.PVSRK......KLQLVGITALLLASKY.......................EEMF..SPNIEDFVYIT..............DN..AYTSSQIREMETLILKELKFELG CCNB2_CHICK/141-266 DIYLYLRQLEL..QQSVRPHYL..DG.KT...ING.RMRAILVDW...LVQVHSRFQLLQETLYMCVAVMDRFLQ.SH.PVPRK......RLQLVGVTALLLASKY.......................EEMY..SPDIADFVYIT..............DN..AYNSAEVREMEITILKELNFDLG A0BXX7_PARTE/85-212 EILQHLLIEEN..KYTI.NQYMTPEQQPD...INI.KMRAILVDW...LIDVHAKFKLKDETLYITISLIDRYLA.LA.QVTRM......RLQLVGVAALFIACKY.......................EEIY..PPALKDFVYIT..............DN..AYVKSDVLEMEGLMLQALNFNIC Q6BFS2_PARTE/82-210 EIYTYLLTQEE..KYLVSNNYMNEQQQPD...LNA.RMRAILLDW...LIDVHLKFKLRDETLYVTTYLIDRFLN.FK.TTTRQ......QLQLVGVASLFIACKY.......................EEIY..PPDLKDFVYIT..............DN..AYTKQDVLEMEGQILQTLDFSIT CG21_CANAL/208-334 EIFSYYYELET..RMLPDPQYL..FKQTL...LKP.RMRSILVDW...LVEMHLKFKLLPESLFLAVNVMDRFMS.VE.VVQID......KLQLLATAALFTAAKY.......................EEVF..SPSVKNYAYFT..............DG..SYTPEEVVQAEKYMLTILNFDLN CGS5_YEAST/165-294 EIFAFLYRREL..ETLPSHNYL..LDKTSKYYLRP.SMRTILVDW...LVEVHEKFQCYPETLFLSINLMDRFLA.KN.KVTMN......KLQLLAVTSLFIAAKF.......................EEVN..LPKLAEYAYIT..............DG..AASKNDIKNAEMFMLTSLEFNIG CGS6_YEAST/123-252 SIFSHLYEKEI..QMLPTHNYL..MDTQSPYHLKS.SMRALLIDW...LVEVHEKFHCLPETLFLAINLLDRFLS.QN.VVKLN......KLQLLCITCLFIACKF.......................EEVK..LPKITNFAYVT..............DG..AATVEGIRKAELFVLSSLGYNIS CG21_YEAST/212-337 DIFDYLHHLEI..ITLPNKANL..YKHKN...IK..QNRDILVNW...IIKIHNKFGLLPETLYLAINIMDRFLC.EE.VVQLN......RLQLVGTSCLFIASKY.......................EEIY..SPSIKHFAYET..............DG..ACSVEDIKEGERFILEKLDFQIS CG22_YEAST/232-357 DIFEYLHQLEV..ITLPKKEDL..YQHRN...IH..QNRDILVNW...LVKIHNKFGLLPETLYLAINIMDRFLG.KE.LVQLD......KLQLVGTSCLFIASKY.......................EEVY..SPSIKHFASET..............DG..ACTEDEIKEGEKFILKTLKFNLN CG24_CANAL/234-360 EIFNYLHELEN..KFTPDPNYM..DFQDD...LKW.EMRAVLIDW...VVQVHARFNLFSETLYLTVNYIDRFLS.KR.RVSLS......RFQLVGAVALFIAAKY.......................EEIN..CPTVQEIAYMA..............DN..AYSIDEFLKAERFMIDVLEFDLG CG23_YEAST/171-297 EIFEYMRKLED..LYKPNPYYM..DKQPE...LRW.SFRSTLIDW...IVQVHEKFQLLPETLYLCINIIDRYLC.KE.VVPVN......KFQLVGAASLFIAAKY.......................EEIN..CPTIKDFVYMS..............EN..CYSRNDLLDAERTILNGLEFELG CG24_YEAST/210-336 DIFYYLRELEV..KYRPNPYYM..QNQVE...LTW.PFRRTMIDW...LVQLHFRFQLLPETLYLTINIVDRFLS.KK.TVTLN......RFQLVGVSALFIAAKF.......................EEIN..CPTLDDLVYML..............EN..TYTRDDIIRAEQYMIDTLEFEIG CG22_SCHPO/139-265 EIFEYIRKLDL..KCLPNPKYM..DQQKE...LTW.KMREILNEW...LVEIHSNFCLMPETLYLAVNIIDRFLS.RR.SCSLS......KFQLTGITALLIASKY.......................EEVM..CPSIQNFVYMT..............DG..AFTVEDVCVAERYMLNVLNFDLS M7PCR8_PNEMU/176-302 EIMSYMRELEV..LTLPLPDYM..DRQKE...LQW.KMRGILVDW...LIEVHAKFRLLPETLFLSVNIIDRFLS.LR.VCSLP......KLQLVGITALFIAAKY.......................EEVM..CPSIQNFMYMA..............DG..GYTNEEILKAEQYVLQVLGYDMS CG21_EMENI/211-337 EIFDYLRELEM..ETLPNPDYI..DHQPD...LEW.KMRGILVDW...LIEVHTRFRLLPETLFLAVNIIDRFLS.AE.VVALD......RLQLVGVAAMFIASKY.......................EEVL..SPHVANFSHVA..............DE..TFSDKEILDAERHILATLEYNMS CG23_SCHPO/206-332 DIFEYLNELEI..ETMPSPTYM..DRQKE...LAW.KMRGILTDW...LIEVHSRFRLLPETLFLAVNIIDRFLS.LR.VCSLN......KLQLVGIAALFIASKY.......................EEVM..CPSVQNFVYMA..............DG..GYDEEEILQAERYILRVLEFNLA CG21_SCHPO/166-292 EIFHYMQSLER..KLAPPPNYM..SVQQE...IDW.VTRHMLVDW...IVQVQIHFRLLPETLFLAVNLIDRFLS.IK.VVSLQ......KVQLVGLSALLIACKY.......................EEIH..PPSIYNFAHVV..............QG..IFTVDEIIRAERYMLMLLDFDIS REM1_SCHPO/145-271 EILSHMEKLEI..RFMPDYRHM..SAQPY...YVT.EMRASVINW...IVGVHTCINLLPESLFLSINVLDRFLS.LQ.NVPAS......KMKLCGATALFIACKY.......................EEIH..PPTVKDLEIVL..............EG..EWIGEDICGMEKYMLMVLQYQLG CCNF_MOUSE/282-406 SVCQLFQASQA....VNKQQIF..SVQKG...LSD.TMRYILIDW...LVEVATMKDFTSLCLHLTVECVDRYLR.RR.LVPRY......KLQLLGIACMVICTRFI.....................SKEIL....TIREAVWLT..............DN..TYKYEDLVRVMGEIISALEGKIR I1K835_SOYBN/85-214 DIHGYLREMEMQNKRRPMVDYI.EKVQKI...VTP.TMRAILVDW...LVEVAVEYKLLSDTLHLSVSYIDRFLS.VN.PVSKS......RLQLLGVSSMLIAAKY.......................EEMD..PPGVDEFCSIT..............DH..TYDKTEVVKMEADILKSLKFEMG J3KY10_ORYBR/200-327 DIYMHLREAET..RKRPSTDFM.ETIQKD...VNP.SMRAILIDW...LVEVAEEYRLVPDTLYLTVNYIDRYLS.GN.EINRQ......RLQLLGVACMLIAAKY.......................EEIC..APQVEEFCYIT..............DN..TYFRDEVLEMEASVLNYLKFEMT M4E4A3_BRARP/154-281 DIYNHLRAAEA..KKQPAVDYM.ATVQKD...VNS.TMRGILVDW...LVEVSEEYRLVPETLYLTVNYIDRYLS.GN.VISRQ......KLQLLGVACMMIAAKY.......................EEVC..APQVEEFCYIT..............DN..TYLKDEVLDMESAVLNYLKFEMS CCA22_ARATH/175-302 DIYDNIHVAEL..QQRPLANYM.ELVQRD...IDP.DMRKILIDW...LVEVSDDYKLVPDTLYLTVNLIDRFLS.NS.YIERQ......RLQLLGVSCMLIASKY.......................EELS..APGVEEFCFIT..............AN..TYTRPEVLSMEIQILNFVHFRLS Q39878_SOYBN/207-334 DIYSNIRVTEL..QRKPLTNYM.DKLQKD...INP.SMRGILVDW...LVEVSEEYKLVPDTLYLTVNLIDRYLS.TR.LIQKQ......KLQLLGVTCMLIASKY.......................EEMC..APRVEEFCFIT..............DN..TYTKEEVLKMEREVLNLVHFQLS T1EGC7_HELRO/166-291 DILTYGKEAEQ..RYMAKANYM..ERQSD...INH.SMRSILVDW...LVEVADEYKLKRETFFLAVNYIDRFLS.MM.SVIRC......RLQLLGAAAMFIAAKY.......................EEIY..PPDVAEFVYIT..............DD..TYTMKQVLQMEQAILKTLNF.LV CCNA1_CAEEL/215-341 DIIKYMLHRQT..KNRASHECF..DIQSQ...VNE.EMRTILIDW...FSDVVKEYNFQKETFHLAVSLVDRALS.MF.NIDKM......RFQLVGTTSMMIAVKY.......................EEIF..PPEIEDFALIT..............DN..TYRVPDILLMERFLLGKFDFVVA CCNA_DROME/206-332 DILEYFRESEK..KHRPKPLYM..RRQKD...ISH.NMRSILIDW...LVEVSEEYKLDTETLYLSVFYLDRFLS.QM.AVVRS......KLQLVGTAAMYIAAKY.......................EEIY..PPEVGEFVFLT..............DD..SYTKAQVLRMEQVILKILSFDLC W4XJF2_STRPU/207-333 EIYQYLKTAES..KHRPKHGYM..RKQPD...ITN.SMRCILVDW...LVEVSEEYRLHNETLYLAAAFIDRFLS.QM.SVLRA......KLQLVGTASMFVASKY.......................EEIY..PPDVKEFVYIT..............DD..TYSIKQVLRMEHLILKVLSFDLA CCNA2_MOUSE/171-297 DIHTYLREMEV..KCKPKVGYM..KRQPD...ITN.SMRAILVDW...LVEVGEEYKLQNETLHLAVNYIDRFLS.SM.SVLRG......KLQLVGTAAMLLASKF.......................EEIY..PPEVAEFVYIT..............DD..TYSKKQVLRMEHLVLKVLAFDLA #=GR CCNA2_MOUSE/171-297 SS HHHHHHHHHHH..HT---TTGG..GG-SS...--H.HHHHHHHHH...HHHHHHHTT--HHHHHHHHHHHHHHHC.C-.---CC......CHHHHHHHHHHHHHHH.......................H-SS..---HHHHHHHT..............TT..SS-HHHHHHHHHHHHHHHTT--- E9QJ66_DANRE/140-266 DIHRYLRECEV..KYRPKPGYM..RKQPD...ITN.CMRVILVDW...LVEVGEEYKLCSETLYLAVNYLDRFLS.CM.SVLRG......KLQLVGTAAILLAAKY.......................EEVY..PPEVDEFVYIT..............DD..TYTKKQLLRMEQHLLRVLAFDMT CCNA1_HUMAN/214-340 EIYQYLREAEI..RHRPKAHYM..KKQPD...ITE.GMRTILVDW...LVEVGEEYKLRAETLYLAVNFLDRFLS.CM.SVLRG......KLQLVGTAAMLLASKY.......................EEIY..PPEVDEFVYIT..............DD..TYTKRQLLKMEHLLLKVLAFDLT CG12_YEAST/43-195 EISTNVIAQSC..KFKPNPKLI..DQQPE...MNPVETRSNIITF...LFELSVVTRVTNGIFFHSVRLYDRYCS.KR.IVLRD......QAKLVVATCLWLAAKTWGGCNHIINNVVIPTGGRFYGPNPRAR..IPRLSELVHYC..............GDGQVFDESMFLQMERHILDTLNWNIY PUC1_SCHPO/99-227 DIIHHLITREK..NFLLNVHLS..NQQPE...LRW.SMRPALVNF...IVEIHNGFDLSIDTLPLSISLMDSYVS.RR.VVYCK......HIQLVACVCLWIASKF.......................HETEDRVPLLQELKLAC..............KN..IYAEDLFIRMERHILDTLDWDIS CG13_CANAL/44-172 EMLHHLLSVEA..KTLPNLSLI..EQQPE...IKL.GMRPLLLDF...LMEVITILSLSRSTFPLTVNLIDRYCS.TR.IVKKQ......HYQLLGLTSLWISCKN.......................LDSKFKVPTLNDLRKIC..............VD..SYYKELFVEMEKHILKSLEWVVN CG11_CANAL/44-172 DIVNTLSQLES..LTLVNPAMI..DLQPE...IQW.FMRPFLLDF...LIELHSSFKLQPTTLFLCLNIIDRYCA.KR.IVFKR......HYQLVGCTALWIASKY.......................EDKKSRVPTLKELTIMC..............RN..AYDEEMFVQMEMHILSTLDWSIG CGH2_SHV21/22-148 RVLNNLKLREL...LLPKFTSL.WEIQTE...VTV.DNRTILLTW...MHLLCESFELDKSVFPLSVSILDRYLC.KK.QGTKK......TLQKIGAACVLIGSKI.......................RTVK..PMTVSKLTYLS..............CD..CFTNLELINQEKDILEALKWDTE #=GR CGH2_SHV21/22-148 SS HHHHHHHHHHT...TS---SST.TTT-SS...S-H.HHHHHHHHH...HHHHHHHTT--TTHHHHHHHHHHHHHH.HS.---TT......THHHHHHHHHHHHHHH.......................HSSS..---HHHHHHTT..............TT..SS-HHHHHHHHHHHHHHTTT--- VCYCL_HHV8P/21-147 .IFYNILEIEP..RFLTSDSVFGTFQQS....LTS.HMRKLLGTW...MFSVCQEYNLEPNVVALALNLLDRLLL.IK.QVSKE......HFQKTGSACLLVASKL.......................RSLT..PISTSSLCYAA..............AD..SFSRQELIDQEKELLEKLAWRTE CCND_CAEEL/72-201 DMRAFYNCMEYEEALQPNYHYF.TGVQEN...ITP.FHREQAIDW...IYDVAKEENCDGDVFLLAVSLIDRFMS.VQ.NILKH......DIQMIAGVALFIASKL.......................KAPH..PMTASKIAYYS..............DN..SCPIDMILQWELLIVTTLQWETE Q7KUZ5_DROME/153-280 ..LENFLKVEEKHHKIPDTYF...SIQKD...ITP.PMRKIVAEW...MMEVCAEENCQEEVVLLALNYMDRFLS.SK.SVRKT......QLQILAAACLLLASKL.......................REPSCRALSVDLLVVYT..............DN..SIYKDDLIKWELYVLSRLGWDLS CCND1_RAT/26-153 RVLRAMLKTEE..TCAPSVSYF.KCVQRE...IVP.SMRKIVATW...MLEVCEEQKCEEEVFPLAMNYLDRFLS.LE.PLKKS......RLQLLGATCMFVASKM.......................KETI..PLTAEKLCIYT..............DN..SIRPEELLQMELLLVNKLKWNLA CCND2_MOUSE/24-151 RVLQNLLTIEE..RYLPQCSYF.KCVQKD...IQP.YMRRMVATW...MLEVCEEQKCEEEVFPLAMNYLDRFLA.GV.PTPKT......HLQLLGAVCMFLASKL.......................KETI..PLTAEKLCIYT..............DN..SVKPQELLEWELVVLGKLKWNLA CCND3_HUMAN/26-153 RVLQSLLRLEE..RYVPRASYF.QCVQRE...IKP.HMRKMLAYW...MLEVCEEQRCEEEVFPLAMNYLDRYLS.CV.PTRKA......QLQLLGAVCMLLASKL.......................RETT..PLTIEKLCIYT..............DH..AVSPRQLRDWEVLVLGKLKWDLA #=GR CCND3_HUMAN/26-153 SS HHHHHHHHHGG..GGS-SS--T.TTSTTT...--H.HHHHHHHHH...HHHHHHHTT--TTHHHHHHHHHHHHHH.H-.---GG......GHHHHHHHHHHHHHHH.......................H-SS..---TTHHHHHT..............TT..SS-HHHHHHHHHHHHHHTTT--- Q9VZP3_DROME/42-165 DIFLTMREQEL.............SRRPLFYLSPQLNERRRMLQL...LKLATSAHKLSRCALHLAVYYMDRFVD.YY.KIRPD......KLLLVAITCLHIAAQI.......................ENTDAFIPRYSEMNRLV..............KN..AYTAFEYKAVERKILCFLNFELI SSN8_YEAST/45-176 DSKQNGIEQSITKNIPITHRDLHYDKDYN........LRIYCYFL...IMKLGRRLNIRQYALATAHIYLSRFLI.KA.SVREI......NLYMLVTTCVYLACKV.......................EEC...PQYIRTLVSEART..........LWPEFIPPDPTKVTEFEFYLLEELESYLI CCC11_ORYSJ/4-144 ....NFWTSSHCKQLLDQEDVDKVPQADSDRGITLEEFRLVKIHMSFHIWRLAQQVKVRQRVIATAVTYFRRVYT.RK.SMTEY......DPRLVAPTCLYLASKV.......................EES...TVQARLLVFYIKKM........CASDEKYRFEIKDILEMEMKLLEALDYYLV CCNT_DROME/42-176 DKIWYFSNDQL.ANSPSRRCGIKGDDELQ........YRQMTAYL...IQEMGQRLQVSQLCINTAIVYMHRFYA.FH.SFTHF......HRNSMASASLFLAAKV.......................EEQ...PRKLEHVIRAANKCL......PPTTEQNYAELAQELVFNENVLLQTLGFDVA CCT12_ARATH/28-169 IIPWFFSREEIERNSPSRRDGIDLKTETR........LRDSYCTF...LEILGERLKVPQVTIATAIFFCHRFFL.RQ.SHAKN......DRQTIATVCMLLAGKV.......................EET...PVTLEDVIIASYERIHKKDLAGAQRKEVYDQQKELVLIGEELVLSTLNFDLC Q9VE72_DROME/6-144 DVMSMQQHVELNKAQTMKPIDYRKMNKPG...........VVPMY...IFECAAKLKMKPLTAACAAIVFHRFFR....EVKASD....YDEFLIAAGSLYLAGKI.......................KEDE..SVKIRDVINVAYCTLNRGNDPVDLNDEYWSM.RDAIVQAELLITRTLCFDLN PCL1_YEAST/19-152 DIIKFLTDTTL..RVVPSSNYPTPPGSPG...EKHLTRLPSLMTF...ITRLVRYTNVYTPTLLTAACYLNKLKR....ILPRDATGLPSTIHRIFLACLILSAKF.......................HNDS..SPLNKHWARYT..............DG..LFTLEDINLMERQLLQLLNWDLR PCL2_YEAST/18-146 EMVQYLASTTASIIKIKKTNSMIDIALPA..........PPLTKF...INRLIKHSNVQTPTLMATSVYLAKLRS....IIPSNVYGIETTRHRIFLGCLILAAKT.......................LNDS..SPLNKHWAEYT..............DG..LLILREVNTIERELLEYFDWDVT PCL9_YEAST/19-146 EMIQFLATSTASIIKIRENNNPIQGCRP...........PDLSIF...IKNVVIQSNVQTPTLMATSVYLNKLKS....VIPKNVYGINTTRHRIFLGCLILAAKT.......................LNDS..SPWNKHWTTYT..............EG..LLRIREVNTIERELLEYLNWDVR CCU41_ARATH/23-148 RVAESNDLTRRVATQSQRVSVFHGLSRPT..........ITIQSY...LERIFKYANCSPSCFVVAYVYLDRFTH.RQPSLPINS....FNVHRLLITSVMVAAKF................................LDDLYYNNAYY.......AKVG....GISTKEMNFLELDFLFGLGFELN Q9VKF0_DROME/205-327 DIFD............EKLHPLTHDQVPDNYDTHNPEHRQ.IYKF...VRTLFNAAQLTAECAIITLVYLERLLTYAELDVGPC......NWKRMVLGAILLASKV................................WDDQAVWNVDYC......QILK....DITVEDMNELERQFLELLQFNIN CCD11_ARATH/50-182 DSIACFIEDER..HFVPGHDYLSRFQTRS...LDA.SAREDSVAW...ILKVQAYYNFQPLTAYLAVNYMDRFLY.AR.RLPETS...GWPMQLLAVACLSLAAKM.......................EEIL..VPSLFDFQVA...............GVKYLFEAKTIKRMELLVLSVLDWRLR CCD21_ARATH/65-197 DRIKEMLVREI..EFCPGTDYVKRLLSGD...LDL.SVRNQALDW...ILKVCAHYHFGHLCICLSMNYLDRFLT.SY.ELPKDK...DWAAQLLAVSCLSLASKM.......................EETD..VPHIVDLQVE...............DPKFVFEAKTIKRMELLVVTTLNWRLQ CCD41_ARATH/45-178 EIIMEMVEKEK..QHLPSDDYIKRLRSGD...LDLNVGRRDALNW...IWKACEVHQFGPLCFCLAMNYLDRFLS.VH.DLPSGK...GWILQLLAVACLSLAAKI.......................EETE..VPMLIDLQVG...............DPQFVFEAKSVQRMELLVLNKLKWRLR Q9SMD4_SOLLC/51-182 EELTSLFSKET..EYEISYNVLEK....N...QSFISSRRESVEW...ILKTTAYYSFSAQTGFLAVNYFDRFLL..F.SFNQSLNHKPWMNQLVAVTCLSLAAKV.......................EETD..VPLLLDLQVE...............ESGFLFESKTIQRMEMLILSTLKWKMN Q9S7H9_SOLLC/61-190 DELATLLSKEN..EFHLGFQSLIS....D...GSLMGARKEALDW...MLRVIAYYGFTATTAVLAVNYFDRFVS.GW.CFQKDK...PWMSQLAAVACLSIAAKV.......................EETQ..VPLLLDLQVA...............DSRFVFEAKTIQRMELLVLSTLKWKMN CCD33_ARATH/59-186 DELSTLISKQE........PCLYDEILDD...EFLVLCREKALDW...IFKVKSHYGFNSLTALLAVNYFDRFIT.SR.KFQTDK...PWMSQLTALACLSLAAKV.......................EEIR..VPFLLDFQVE...............EARYVFEAKTIQRMELLVLSTLDWRMH CCD61_ARATH/26-154 TLPHSLFLVEF..QHMPSSHYFHSLKSSA...FLL.SNRNQAISS...ITQYSRKFD.DPSLTYLAVNYLDRFLS.SE.DMPQSK...PWILKLISLSCVSLSAKM.......................RKPD...MSVSDLPVE...............GE..FFDAQMIERMENVILGALKWRMR CCNE_DROME/330-459 DVWRLMCHRDEQDSRLRSISML..EQHPG...LQP.RMRAILLDW...LIEVCEVYKLHRETFYLAVDYLDRYLHVAH.KVQKT......HLQLIGITCLFVAAKV.......................EEIY..PPKIGEFAYVT..............DG..ACTERDILNHEKILLQALDWDIS CCNE2_MOUSE/112-239 EVWQNMLQKEN..RYVHDKHFQ..VLHSD...LEP.QMRSILLDW...LLEVCEVYTLHRETFYLAQDFFDRFMLTQK.DVNKN......MLQLIGITSLFIASKL.......................EEIY..APKLQEFAYVT..............DG..ACSEVDILKMELNILKALKWELC CCNE1_CHICK/112-239 DVWKNMINKEE..TYVRDKLYM..QRHPL...LQP.KMRTILLDW...LMEVCEVYKLYRETFYLAQDFFDRFMATQQ.NVVKT......LLQLIGISSLFIAAKL.......................EEIY..PPKLHQFAYVT..............DG..ACTEDEILSMELIIMKALNWNLN CCNE1_MOUSE/113-240 EVWRIMLNKEK..TYLRDEHFL..QRHPL...LQA.RMRAVLLDW...LMEVCEVYKLHRETFYLAQDFFDRYMASQH.NIIKT......LLQLIGISALFIASKL.......................EEIY..PPKLHQFAYVT..............DG..ACSGDEILTMELMMMKALKWRLS A0A0R4IZF8_DANRE/117-244 EVWNNLLGKDK..LYLRDTRVM..ERHPN...LQP.KMRAILLDW...LMEVCEVYKLHRETFYLGQDYFDRFMATQE.NVLKT......TLQLIGISCLFIAAKM.......................EEIY..PPKVHQFAYVT..............DG..ACTEDDILSMEIIIMKELNWSLS F6QUN0_XENTR/114-241 DVWRNMLNKDR..TYLRDKNFF..QKHPQ...LQP.NMRAILLDW...LMEVCEVYKLHRETFYLGQDFFDRFMATQK.NVIKS......RLQLIGITSLFIAAKL.......................EEIY..PPKLHQFAFIT..............DG..ACTEDEITSMELIIMKDLDWCLS W4XEA0_STRPU/126-253 EVWTIMTRKEA..LCPRKHDCL..KSHPS...LGE.RMRAILLDW...LIEVCEVYRLHRESFYLAADFVDRYLAAKE.NVPKT......KLQLIGITSLFVAAKL.......................EEIY..PPKLHEFAYVT..............DG..ACTDDQILDQELIMLMTLNWDLT CCNE_CAEEL/232-360 KVWSLMVKRDE..IPRATRFLL..GNHPD...MDD.EKRRILIDW...MMEVCESEKLHRETFHLAVDYVDRYLESSNVECSTD......NFQLVGTAALFIAAKY.......................EEIY..PPKCIDFAHLT..............DS..AFTCDNIRTMEVLIVKYIGWSLG #=GC SS_cons HHHHHHHHHHC..HTS-STTCT.TTCTSS...S-H.HHHHHHHHH...HHHHHHHTT--TTHHHHHHHHHHHHHH.HS.---CC......CHHHHHHHHHHHHHHH.......................HSSS..---HHHHHHHT..............TT..SS-HHHHHHHHHHHHHHTTT--- #=GC seq_cons -IapahpptEt..phhsp.sYh..ppps-...ls..pMRsILlDW...Ll-VppcacLhtETLaLulshlDRFLu.tp.sls+s......cLQLlGlsulhlAuKa.......................EElh..sPplp-hshlo..............Ds..saopcpllpMEphlLpsLpasls // """, ) def check_alignment_pfam9(self, alignment): """Check the alignment obtained by parsing Pfam record SH3_11.""" self.assertEqual(alignment.annotations["identifier"], "SH3_11") self.assertEqual(alignment.annotations["accession"], "PF18103.3") self.assertEqual( alignment.annotations["definition"], "Retroviral integrase C-terminal SH3 domain", ) self.assertEqual( alignment.annotations["author"], ["El-Gebali S;0000-0003-1378-5495"] ) self.assertEqual(alignment.annotations["source of seed"], "ECOD:EUF00899") self.assertEqual(alignment.annotations["gathering method"], "25.00 25.00;") self.assertEqual(alignment.annotations["trusted cutoff"], "25.20 78.10;") self.assertEqual(alignment.annotations["noise cutoff"], "24.90 24.20;") self.assertEqual( alignment.annotations["build method"], "hmmbuild HMM.ann SEED.ann" ) self.assertEqual( alignment.annotations["search method"], "hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq", ) self.assertEqual(alignment.annotations["type"], "Domain") self.assertEqual( alignment.annotations["wikipedia"], ["Integrase", "SH3_domain"] ) self.assertEqual(alignment.annotations["clan"], "CL0010") self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "20118915") self.assertEqual( alignment.annotations["references"][0]["title"], "Retroviral intasome assembly and inhibition of DNA strand transfer.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P;", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Nature. 2010;464:232-236.", ) self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0]["reference"], "INTERPRO; IPR040903;", ) self.assertEqual( alignment.annotations["database references"][1]["reference"], "SO; 0000417; polypeptide_domain;", ) self.assertEqual( alignment.annotations["comment"], "This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure [1].", ) self.assertEqual(len(alignment.sequences), 1) self.assertEqual(alignment.sequences[0].id, "POL_SFVCP/1064-1126") self.assertEqual(alignment.sequences[0].annotations["accession"], "Q87040.1") self.assertEqual( alignment.sequences[0].seq, "RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ", ) self.assertEqual( alignment.column_annotations["consensus sequence"], "RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ", ) self.assertTrue(np.array_equal(alignment.coordinates, np.array([[0, 63]]))) self.assertEqual( str(alignment), """\ POL_SFVCP 0 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPT POL_SFVCP 60 SHQ 63 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID SH3_11 #=GF AC PF18103.3 #=GF DE Retroviral integrase C-terminal SH3 domain #=GF AU El-Gebali S;0000-0003-1378-5495 #=GF SE ECOD:EUF00899 #=GF GA 25.00 25.00; #=GF TC 25.20 78.10; #=GF NC 24.90 24.20; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF CL CL0010 #=GF WK Integrase #=GF WK SH3_domain #=GF RN [1] #=GF RM 20118915 #=GF RT Retroviral intasome assembly and inhibition of DNA strand transfer. #=GF RA Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P; #=GF RL Nature. 2010;464:232-236. #=GF DR INTERPRO; IPR040903; #=GF DR SO; 0000417; polypeptide_domain; #=GF CC This is the carboxy-terminal domain (CTD) found in retroviral #=GF CC integrase, an essential retroviral enzyme that binds both termini of #=GF CC linear viral DNA and inserts them into a host cell chromosome. The #=GF CC CTD adopts an SH3-like fold. Each CTD makes contact with the #=GF CC phosphodiester backbone of both viral DNA molecules, essentially #=GF CC crosslinking the structure [1]. #=GF SQ 1 #=GS POL_SFVCP/1064-1126 AC Q87040.1 POL_SFVCP/1064-1126 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ #=GC seq_cons RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ // """, ) def check_alignment_rfam1(self, alignment): """Check the alignment obtained by parsing Rfam record BTnc005.""" self.assertEqual(alignment.annotations["accession"], "RF04178") self.assertEqual(alignment.annotations["identifier"], "BTnc005") self.assertEqual( alignment.annotations["definition"], "Bacteroides sRNA BTnc005" ) self.assertEqual( alignment.annotations["author"], [ "Prezza, G", "Ryan, D", "Mädler, G", "Barquist, L; 0000-0003-4732-2667", "Westermann, A", ], ) self.assertEqual( alignment.annotations["source of seed"], "Published; PMID:32678091;" ) self.assertEqual( alignment.annotations["source of structure"], "Published; PMID:32678091;" ) self.assertEqual(alignment.annotations["gathering method"], "174.80") self.assertEqual(alignment.annotations["trusted cutoff"], "179.30") self.assertEqual(alignment.annotations["noise cutoff"], "174.30") self.assertEqual(alignment.annotations["type"], "Gene; sRNA;") self.assertEqual(alignment.annotations["build method"], "cmbuild -F CM SEED") self.assertEqual( alignment.annotations["calibration method"], "cmcalibrate --mpi CM" ) self.assertEqual( alignment.annotations["search method"], "cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB", ) self.assertEqual(len(alignment.annotations["database references"]), 1) self.assertEqual( alignment.annotations["database references"][0], {"reference": "SO; 0000655; ncRNA;"}, ) self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "32678091") self.assertEqual( alignment.annotations["references"][0]["title"], "A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Nat Commun. 2020;11:3557.", ) self.assertEqual( alignment.annotations["comment"], "An uncharacterized small RNA discovered in Bacteroides thetaiotaomicron [1]", ) self.assertEqual( alignment.annotations["wikipedia"], ["Bacteroides_thetaiotaomicron_sRNA"] ) self.assertEqual(len(alignment.sequences), 3) self.assertEqual(alignment.sequences[0].id, "AE015928.1/72774-72978") self.assertEqual(alignment.sequences[1].id, "CP000139.1/2819055-2819247") self.assertEqual(alignment.sequences[2].id, "FP929033.1/4930704-4930908") self.assertEqual( alignment.sequences[0].seq, "GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCAGAACCUACUGGACAAAACAGGACAGUAAGUGGACAAAAACCUACAAAUCAGCGAUUUGUAGGUUUUUU", ) self.assertEqual( alignment.sequences[1].seq, "AAAAGUAAGAGUGUAACAGGAAGAAAGUUGCAGCAUAUACGCGGUGAAUUAUUCGGUGUCAUAGGAGUAGAGUCUUUUGGUAAGAUGCUGAUAAUGAGUAGGGGAGAUGAAAGUUAAUCGUUCCCUGUCUCUCCGCUGGAAAGAAUUGCAAAACAAAGAAAAUCCCUGUAAAUUAAUACUUUACGGGGAUUUU", ) self.assertEqual( alignment.sequences[2].seq, "GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCUGAACUAUCCGGACAAAACCGGGCAAUGAACAGUCAAAUCCCACAAAUUCAAUGAUUUGUGGGACUUUU", ) self.assertEqual( alignment[0], "GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCAGAACCUACUGGACAAAACAGGACAGUAAGUGGACAAAAACCUACAAAUCAGC-GAUUUGUAGGUUUUUU", ) self.assertEqual( alignment[1], "AAAAGUAAGAGUGUAACAGGAAGAAAGUUGCAGCAUAUACGCGGUGAAUUAUUCGGUGUCAUAGGAGUAGAGUCUUUUGGUAAGAUGCUGAUAAUGAGUAGGGGAGAUGAAAGUUAAUCGUUCCCUGUCUCUCCGCUGG---------AAAGAAUUGCAAAACAA--AGA-AAAUCCCUGUAAAUUAAU-ACUUUACGGGGAUUUU", ) self.assertEqual( alignment[2], "GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCUGAACUAUCCGGACAAAACCGGGCAAUGAACAGUCAAA-UCCCACAAAUUCAAUGAUUUGUGGGACUUUU", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], ":::::::::::<<<<<<_________>>>>>>,,,,,,,,((((,,,<<<<<-<<<<<<<----<<<_______>>>------>>>>>>>>>>>><<<<<-<<<<_______________>>>>->>->>>,))))---------------------------------------<<<<<<<<<<<____>>>>>>>>>>>:::::", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "guAAGUAAaAGuGuaaCAGGAAGAAAGuugCaGCAUAUAuGCGGUGAauuaugCgGuguCAUAGgaaUuGAGgauuuauGUAAGaugCuGauaauGaGuaaGGaaccUuAAAGUUAAUCGuuCCCugUCuCUCCGCuGaACuaaCuGGAcAaAAcuGgacAauaAauaGaCAAAacCCcgcaaaucaau.gauuugcgGGguUUUU", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 139, 148, 165, 167, 170, 171, 174, 175, 189, 189, 205], [0, 139, 139, 156, 156, 159, 159, 162, 163, 177, 177, 193], [0, 139, 148, 165, 167, 170, 171, 174, 174, 188, 189, 205], ] ), ) ) self.assertEqual( str(alignment), """\ AE015928. 0 GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUC CP000139. 0 AAAAGUAAGAGUGUAACAGGAAGAAAGUUGCAGCAUAUACGCGGUGAAUUAUUCGGUGUC FP929033. 0 GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUC AE015928. 60 AUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCG CP000139. 60 AUAGGAGUAGAGUCUUUUGGUAAGAUGCUGAUAAUGAGUAGGGGAGAUGAAAGUUAAUCG FP929033. 60 AUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCG AE015928. 120 UUCCCUGUCUCUCCGCAGAACCUACUGGACAAAACAGGACAGUAAGUGGACAAAAACCUA CP000139. 120 UUCCCUGUCUCUCCGCUGG---------AAAGAAUUGCAAAACAA--AGA-AAAUCCCUG FP929033. 120 UUCCCUGUCUCUCCGCUGAACUAUCCGGACAAAACCGGGCAAUGAACAGUCAAA-UCCCA AE015928. 180 CAAAUCAGC-GAUUUGUAGGUUUUUU 205 CP000139. 168 UAAAUUAAU-ACUUUACGGGGAUUUU 193 FP929033. 179 CAAAUUCAAUGAUUUGUGGGACUUUU 205 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID BTnc005 #=GF AC RF04178 #=GF DE Bacteroides sRNA BTnc005 #=GF AU Prezza, G #=GF AU Ryan, D #=GF AU Mädler, G #=GF AU Barquist, L; 0000-0003-4732-2667 #=GF AU Westermann, A #=GF SE Published; PMID:32678091; #=GF SS Published; PMID:32678091; #=GF GA 174.80 #=GF TC 179.30 #=GF NC 174.30 #=GF BM cmbuild -F CM SEED #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB #=GF TP Gene; sRNA; #=GF WK Bacteroides_thetaiotaomicron_sRNA #=GF CB cmcalibrate --mpi CM #=GF RN [1] #=GF RM 32678091 #=GF RT A high-resolution transcriptome map identifies small RNA regulation #=GF RT of metabolism in the gut microbe Bacteroides thetaiotaomicron. #=GF RA Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ #=GF RL Nat Commun. 2020;11:3557. #=GF DR SO; 0000655; ncRNA; #=GF CC An uncharacterized small RNA discovered in Bacteroides #=GF CC thetaiotaomicron [1] #=GF SQ 3 AE015928.1/72774-72978 GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCAGAACCUACUGGACAAAACAGGACAGUAAGUGGACAAAAACCUACAAAUCAGC-GAUUUGUAGGUUUUUU CP000139.1/2819055-2819247 AAAAGUAAGAGUGUAACAGGAAGAAAGUUGCAGCAUAUACGCGGUGAAUUAUUCGGUGUCAUAGGAGUAGAGUCUUUUGGUAAGAUGCUGAUAAUGAGUAGGGGAGAUGAAAGUUAAUCGUUCCCUGUCUCUCCGCUGG---------AAAGAAUUGCAAAACAA--AGA-AAAUCCCUGUAAAUUAAU-ACUUUACGGGGAUUUU FP929033.1/4930704-4930908 GUAAGUAAAAGUGUAACAGGAAGAAAGUUGCAGCAUAUAUGCGGUGAAUUAUGCGGUGUCAUAGGAAUUGAGGAUUUAUGUAAGAUGCUGAUAAUGAGUAAGGAACCUUAAAGUUAAUCGUUCCCUGUCUCUCCGCUGAACUAUCCGGACAAAACCGGGCAAUGAACAGUCAAA-UCCCACAAAUUCAAUGAUUUGUGGGACUUUU #=GC SS_cons :::::::::::<<<<<<_________>>>>>>,,,,,,,,((((,,,<<<<<-<<<<<<<----<<<_______>>>------>>>>>>>>>>>><<<<<-<<<<_______________>>>>->>->>>,))))---------------------------------------<<<<<<<<<<<____>>>>>>>>>>>::::: #=GC RF guAAGUAAaAGuGuaaCAGGAAGAAAGuugCaGCAUAUAuGCGGUGAauuaugCgGuguCAUAGgaaUuGAGgauuuauGUAAGaugCuGauaauGaGuaaGGaaccUuAAAGUUAAUCGuuCCCugUCuCUCCGCuGaACuaaCuGGAcAaAAcuGgacAauaAauaGaCAAAacCCcgcaaaucaau.gauuugcgGGguUUUU // """, ) def check_alignment_rfam2(self, alignment): """Check the alignment obtained by parsing Rfam record SraC_RyeA.""" self.assertEqual(alignment.annotations["accession"], "RF00101") self.assertEqual(alignment.annotations["identifier"], "SraC_RyeA") self.assertEqual(alignment.annotations["definition"], "SraC/RyeA RNA") self.assertEqual( alignment.annotations["author"], ["Bateman A; 0000-0002-6982-4660"] ) self.assertEqual(alignment.annotations["source of seed"], "Bateman A") self.assertEqual( alignment.annotations["source of structure"], "Predicted; PFOLD" ) self.assertEqual(alignment.annotations["gathering method"], "37.00") self.assertEqual(alignment.annotations["trusted cutoff"], "37.20") self.assertEqual(alignment.annotations["noise cutoff"], "36.80") self.assertEqual(alignment.annotations["type"], "Gene; sRNA;") self.assertEqual(alignment.annotations["build method"], "cmbuild -F CM SEED") self.assertEqual( alignment.annotations["calibration method"], "cmcalibrate --mpi CM" ) self.assertEqual( alignment.annotations["search method"], "cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB", ) self.assertEqual(alignment.annotations["clan"], "CL00105") self.assertEqual(len(alignment.annotations["database references"]), 1) self.assertEqual( alignment.annotations["database references"][0], {"reference": "SO; 0000655; ncRNA;"}, ) self.assertEqual(len(alignment.annotations["references"]), 2) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "11448770") self.assertEqual( alignment.annotations["references"][0]["title"], "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Curr Biol 2001;11:941-950.", ) self.assertEqual(alignment.annotations["references"][1]["number"], 2) self.assertEqual(alignment.annotations["references"][1]["medline"], "11445539") self.assertEqual( alignment.annotations["references"][1]["title"], "Identification of novel small RNAs using comparative genomics and microarrays.", ) self.assertEqual( alignment.annotations["references"][1]["author"], "Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S", ) self.assertEqual( alignment.annotations["references"][1]["location"], "Genes Dev 2001;15:1637-1651.", ) self.assertEqual( alignment.annotations["comment"], "This RNA was discovered in E. coli during a large scale screens [1-2]. The function of this RNA is unknown. This RNA overlaps RFAM:RF00111 on the opposite strand suggesting that the two may act in a concerted manner.", ) self.assertEqual(alignment.annotations["wikipedia"], ["SraC/RyeA_RNA"]) self.assertEqual(len(alignment.sequences), 13) self.assertEqual(alignment.sequences[0].id, "AL627272.1/127686-127830") self.assertEqual(alignment.sequences[1].id, "CP000653.1/2601613-2601758") self.assertEqual(alignment.sequences[2].id, "AE017042.1/1756200-1756347") self.assertEqual(alignment.sequences[3].id, "CP000034.1/1046100-1046244") self.assertEqual(alignment.sequences[4].id, "CP000647.1/2580976-2581120") self.assertEqual(alignment.sequences[5].id, "AM286415.1/1991675-1991530") self.assertEqual(alignment.sequences[6].id, "CU928145.2/2074283-2074427") self.assertEqual(alignment.sequences[7].id, "CP000970.1/1336993-1336849") self.assertEqual(alignment.sequences[8].id, "AM933172.1/1226335-1226191") self.assertEqual(alignment.sequences[9].id, "AALD02000029.1/37435-37580") self.assertEqual(alignment.sequences[10].id, "AALC02000009.1/70496-70641") self.assertEqual(alignment.sequences[11].id, "AALF02000003.1/121616-121765") self.assertEqual(alignment.sequences[12].id, "AALE02000013.1/38-183") self.assertEqual( alignment.sequences[0].seq, "AAUUAAAAAAAGACCGAAUACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUAAAUCGCCUUGCUCUUUAAGAAUAGAUGACGACGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment.sequences[1].seq, "AGAUAAAAAGAGACCGAAUACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAUAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUAACUACGCCUGACACUCUAAGAAUAGAUGACGACGCCAGGUUUUCCAGUCC", ) self.assertEqual( alignment.sequences[2].seq, "AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGUAUUAAUGUAGGCUUAUUCAGCCGCACUUCUUAAGCGUAGCCGAGUACCGACAUUUCGCCAACCUU", ) self.assertEqual( alignment.sequences[3].seq, "AAUGAAAAAAAGACCGAAUACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUUAGUUGCCUUGCCCUUUAAGAAUAGAUGACGACGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment.sequences[4].seq, "AGAUAAAAAGAGACCGAAUACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUAAGUCGCCUUGCACUAUAAGAAUAGUUUAACGCGUCAGCUUUUCCAGUCC", ) self.assertEqual( alignment.sequences[5].seq, "AAUUAAAAAGAGACCGAAUACGAUUCCUAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAACGUAGGCUUGUUCAGCCAUACUCUUUAAGAGUAGUCGAGGUCAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment.sequences[6].seq, "AGAUAAAAAGAGACCGAACACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUUAGUUGCCUUGCCCUUUAAGAAUAGAUGACGACGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment.sequences[7].seq, "AGAUAAAAAGAGACCGAACACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUUAGUUGCCUUGCUCUUUAAGAAUAGAUGACGACGCCAGAUUUUCCAGUUU", ) self.assertEqual( alignment.sequences[8].seq, "AAAUAAAAAGAGACCGAAUACGAUUCCUGUAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAUGCAGGCUAAAUCGCCUUGCCCUUUAAGAAUAGAUGACGACGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment.sequences[9].seq, "ACUUAAAAAGAGACCGAAUACGAUUCCUAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAACGUAGGCUUGUUCAGCCGUACUACUUAAGCGUAGUCGAGUACAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment.sequences[10].seq, "AGAUAAAAAAAGACCGAAUACGAUUCCUAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAACGUAGGCUUAUUCAGCCGUACUCCUUAAGCGUAGUCGAGUACAUGUAUUUAGCCAACUU", ) self.assertEqual( alignment.sequences[11].seq, "AAUUAAAAAAAGACCGAAUACGAUUCCUAUAUUCGGUCUAGGGAAAUGGCUCUUGGGACAGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUUCAGCCGUACUCCUUAAGCGUAGUCGAGUACAUGUGUUUAGCCAACUU", ) self.assertEqual( alignment.sequences[12].seq, "AGUUAAAAAAAGACCGAAUACGAUUCCUAUAUUCGGUCUAGGGAAAGGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAACGUAGGCUUAUUCAGCCGUACUCCUUAAGCGUAGUCGAGUACAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment[0], "AAUUAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment[1], "AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAUAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAACUAC-GCCUGACACUCUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUCC", ) self.assertEqual( alignment[2], "AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGUAUUAAU----GUAGGCUUAUU-CAGCCGCACUUCUUAAGCGUAGCCGAGUACCGACAUUUCGCCAACCUU", ) self.assertEqual( alignment[3], "AAUGAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment[4], "AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAGU-C-GCCUUGCACUAUAAGAAUAGUUUAACG-CGUCAGCUUUUCCAGUCC", ) self.assertEqual( alignment[5], "AAUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCAUACUCUUUAAGAGUAGUCGAGGU-CAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment[6], "AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment[7], "AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGAUUUUCCAGUUU", ) self.assertEqual( alignment[8], "AAAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU", ) self.assertEqual( alignment[9], "ACUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCGUACUACUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment[10], "AGAUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUAUUUAGCCAACUU", ) self.assertEqual( alignment[11], "AAUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGACAGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUAGCCAACUU", ) self.assertEqual( alignment[12], "AGUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAGGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], ":::::::::::<<<<<<<<<<_______>.>>>>>>>>>,,,,,,,<<<<<<<<______>>>>>>>>,,<<_________>>,,,,,,....,,,<<<_____._.>>>::::::::::::::::::::::::.::::::::::::::::::", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "AauUAAAAAaAGaCCGaauacGAUUCCUg.uauuCGGuCuAGGGAAauGGCuCuUGGGAgaGaGCCguGCGCUAAAAGUUGGCAUUAAu....GuAGGCUuAuU.c.GCCuuaCucuUUAAGaaUAGuuGAguA.CgucaguUUuuCcAauUU", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 100, 101, 101, 128, 128, 146], [0, 29, 30, 89, 89, 100, 100, 101, 102, 129, 130, 148], [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 99, 100, 101, 128, 128, 146], [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 99, 100, 100, 127, 127, 145], [0, 29, 29, 88, 88, 99, 99, 100, 101, 128, 128, 146], [0, 29, 29, 88, 88, 99, 99, 100, 101, 128, 128, 146], [0, 29, 29, 88, 92, 103, 103, 104, 105, 132, 132, 150], [0, 29, 29, 88, 88, 99, 99, 100, 101, 128, 128, 146], ] ), ) ) self.assertEqual( str(alignment), """\ AL627272. 0 AAUUAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG CP000653. 0 AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAU AE017042. 0 AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAG CP000034. 0 AAUGAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG CP000647. 0 AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG AM286415. 0 AAUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAG CU928145. 0 AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG CP000970. 0 AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG AM933172. 0 AAAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAG AALD02000 0 ACUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAG AALC02000 0 AGAUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAG AALF02000 0 AAUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAC AALE02000 0 AGUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAGGGCUCUUGGGAG AL627272. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCUCUUUA CP000653. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAACUAC-GCCUGACACUCUA AE017042. 60 AGAGCCGUGCGCUAAAAGUUGGUAUUAAU----GUAGGCUUAUU-CAGCCGCACUUCUUA CP000034. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUA CP000647. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAGU-C-GCCUUGCACUAUA AM286415. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCAUACUCUUUA CU928145. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUA CP000970. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCUCUUUA AM933172. 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCCCUUUA AALD02000 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCGUACUACUUA AALC02000 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUA AALF02000 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUU-CAGCCGUACUCCUUA AALE02000 59 AGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUA AL627272. 113 AGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU 145 CP000653. 114 AGAAUAGAUGACGA-CGCCAGGUUUUCCAGUCC 146 AE017042. 115 AGCGUAGCCGAGUACCGACAUUUCGCCAACCUU 148 CP000034. 113 AGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU 145 CP000647. 113 AGAAUAGUUUAACG-CGUCAGCUUUUCCAGUCC 145 AM286415. 114 AGAGUAGUCGAGGU-CAUGUGUUUCGCCAACUU 146 CU928145. 113 AGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU 145 CP000970. 113 AGAAUAGAUGACGA-CGCCAGAUUUUCCAGUUU 145 AM933172. 113 AGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU 145 AALD02000 114 AGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU 146 AALC02000 114 AGCGUAGUCGAGUA-CAUGUAUUUAGCCAACUU 146 AALF02000 118 AGCGUAGUCGAGUA-CAUGUGUUUAGCCAACUU 150 AALE02000 114 AGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU 146 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID SraC_RyeA #=GF AC RF00101 #=GF DE SraC/RyeA RNA #=GF AU Bateman A; 0000-0002-6982-4660 #=GF SE Bateman A #=GF SS Predicted; PFOLD #=GF GA 37.00 #=GF TC 37.20 #=GF NC 36.80 #=GF BM cmbuild -F CM SEED #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB #=GF TP Gene; sRNA; #=GF CL CL00105 #=GF WK SraC/RyeA_RNA #=GF CB cmcalibrate --mpi CM #=GF RN [1] #=GF RM 11448770 #=GF RT Novel small RNA-encoding genes in the intergenic regions of #=GF RT Escherichia coli. #=GF RA Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S #=GF RL Curr Biol 2001;11:941-950. #=GF RN [2] #=GF RM 11445539 #=GF RT Identification of novel small RNAs using comparative genomics and #=GF RT microarrays. #=GF RA Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S #=GF RL Genes Dev 2001;15:1637-1651. #=GF DR SO; 0000655; ncRNA; #=GF CC This RNA was discovered in E. coli during a large scale screens #=GF CC [1-2]. The function of this RNA is unknown. This RNA overlaps #=GF CC RFAM:RF00111 on the opposite strand suggesting that the two may act #=GF CC in a concerted manner. #=GF SQ 13 AL627272.1/127686-127830 AAUUAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU CP000653.1/2601613-2601758 AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAUAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAACUAC-GCCUGACACUCUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUCC AE017042.1/1756200-1756347 AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGUAUUAAU----GUAGGCUUAUU-CAGCCGCACUUCUUAAGCGUAGCCGAGUACCGACAUUUCGCCAACCUU CP000034.1/1046100-1046244 AAUGAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU CP000647.1/2580976-2581120 AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAGU-C-GCCUUGCACUAUAAGAAUAGUUUAACG-CGUCAGCUUUUCCAGUCC AM286415.1/1991675-1991530 AAUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCAUACUCUUUAAGAGUAGUCGAGGU-CAUGUGUUUCGCCAACUU CU928145.2/2074283-2074427 AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU CP000970.1/1336993-1336849 AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGAUUUUCCAGUUU AM933172.1/1226335-1226191 AAAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU AALD02000029.1/37435-37580 ACUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCGUACUACUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU AALC02000009.1/70496-70641 AGAUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUAUUUAGCCAACUU AALF02000003.1/121616-121765 AAUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGACAGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUAGCCAACUU AALE02000013.1/38-183 AGUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAGGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU #=GC SS_cons :::::::::::<<<<<<<<<<_______>.>>>>>>>>>,,,,,,,<<<<<<<<______>>>>>>>>,,<<_________>>,,,,,,....,,,<<<_____._.>>>::::::::::::::::::::::::.:::::::::::::::::: #=GC RF AauUAAAAAaAGaCCGaauacGAUUCCUg.uauuCGGuCuAGGGAAauGGCuCuUGGGAgaGaGCCguGCGCUAAAAGUUGGCAUUAAu....GuAGGCUuAuU.c.GCCuuaCucuUUAAGaaUAGuuGAguA.CgucaguUUuuCcAauUU // """, ) def check_alignment_rfam3(self, alignment): """Check the alignment obtained by parsing Rfam record McaS.""" self.assertEqual(alignment.annotations["accession"], "RF00115") self.assertEqual(alignment.annotations["identifier"], "McaS") self.assertEqual(alignment.annotations["previous identifier"], "IS061;") self.assertEqual(alignment.annotations["definition"], "McaS/IsrA RNA") self.assertEqual( alignment.annotations["author"], ["Argasinska J; 0000-0003-2678-2824"] ) self.assertEqual(alignment.annotations["source of seed"], "Argasinska J") self.assertEqual( alignment.annotations["source of structure"], "Predicted; 22289118" ) self.assertEqual(alignment.annotations["gathering method"], "42.00") self.assertEqual(alignment.annotations["trusted cutoff"], "42.10") self.assertEqual(alignment.annotations["noise cutoff"], "38.70") self.assertEqual(alignment.annotations["type"], "Gene; sRNA;") self.assertEqual(alignment.annotations["build method"], "cmbuild -n -F CM SEED") self.assertEqual( alignment.annotations["calibration method"], "cmcalibrate --mpi CM" ) self.assertEqual( alignment.annotations["search method"], "cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize 128 CM SEQDB", ) self.assertEqual(alignment.annotations["clan"], "CL00106") self.assertEqual(len(alignment.annotations["database references"]), 3) self.assertEqual( alignment.annotations["database references"][0], {"reference": "SO; 0001263; ncRNA_gene;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "GO; 0005515; protein binding;"}, ) self.assertEqual( alignment.annotations["database references"][2], {"reference": "GO; 0006417; regulation of translation;"}, ) self.assertEqual(len(alignment.annotations["references"]), 4) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "12069726") self.assertEqual( alignment.annotations["references"][0]["title"], "A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB", ) self.assertEqual( alignment.annotations["references"][0]["location"], "Biosystems 2002;65:157-177.", ) self.assertEqual(alignment.annotations["references"][1]["number"], 2) self.assertEqual(alignment.annotations["references"][1]["medline"], "23666921") self.assertEqual( alignment.annotations["references"][1]["title"], "Dual function of the McaS small RNA in controlling biofilm formation.", ) self.assertEqual( alignment.annotations["references"][1]["author"], "Jorgensen MG, Thomason MK, Havelund J, Valentin-Hansen P, Storz G", ) self.assertEqual( alignment.annotations["references"][1]["location"], "Genes Dev. 2013;27:1132-1145.", ) self.assertEqual(alignment.annotations["references"][2]["number"], 3) self.assertEqual(alignment.annotations["references"][2]["medline"], "22289118") self.assertEqual( alignment.annotations["references"][2]["title"], "A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli.", ) self.assertEqual( alignment.annotations["references"][2]["author"], "Thomason MK, Fontaine F, De Lay N, Storz G", ) self.assertEqual( alignment.annotations["references"][2]["location"], "Mol Microbiol. 2012;84:17-35.", ) self.assertEqual(alignment.annotations["references"][3]["number"], 4) self.assertEqual(alignment.annotations["references"][3]["medline"], "26609136") self.assertEqual( alignment.annotations["references"][3]["title"], "Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate.", ) self.assertEqual( alignment.annotations["references"][3]["author"], "van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N", ) self.assertEqual( alignment.annotations["references"][3]["location"], "Nucleic Acids Res. 2016;44:2577-2592.", ) self.assertEqual( alignment.annotations["comment"], "This family consists of several bacterial RNA genes which are found between the abgR and ydaL genes in Escherichia coli and Shigella flexneri.[1] It was discovered using a computational screen of the E. coli genome.[1] Subsequent characterisation of ISO61 region has revealed that the reverse strand is actually a CsrA binding ncRNA called McaS and that it has a role in biofilm formation control.[2] Furthermore, it has been shown that McaS(IsrA) exists as a ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase.[4]", ) self.assertEqual(alignment.annotations["wikipedia"], ["IS061_RNA"]) self.assertEqual(len(alignment.sequences), 4) self.assertEqual(alignment.sequences[0].id, "CP000036.1/1703842-1703937") self.assertEqual(alignment.sequences[1].id, "U00096.3/1405751-1405656") self.assertEqual(alignment.sequences[2].id, "CP000034.1/1309299-1309204") self.assertEqual(alignment.sequences[3].id, "CP011132.1/1732716-1732810") self.assertEqual( alignment.sequences[0].seq, "ACCGGCGCAGAGGAGACAAUGCCGGACUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU", ) self.assertEqual( alignment.sequences[1].seq, "ACCGGCGCAGAGGAGACAAUGCCGGAUUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU", ) self.assertEqual( alignment.sequences[2].seq, "ACCGGUCACCAGGACCCCAGGCCGGAUUUAAGACGAGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU", ) self.assertEqual( alignment.sequences[3].seq, "ACCCGCCACACGGAAUAAUAACGGGAACACAUGAAGGAUAAACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU", ) self.assertEqual( alignment[0], "ACCGGCGCAGAGGAGACAAUGCCGGACUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU", ) self.assertEqual( alignment[1], "ACCGGCGCAGAGGAGACAAUGCCGGAUUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU", ) self.assertEqual( alignment[2], "ACCGGUCACCAGGACCCCAGGCCGGAUUUAAGACGAGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU", ) self.assertEqual( alignment[3], "ACCCGCCACACGGAAUAAUAACGGGAACACAUG-AAGGAUAAACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], ":<<<<<<____________>>>>>>,,,,,,,<<<<<<________>>>>>>-----<<<<<<<<<<-<<_____>>->>>>>>>>>>::::::::", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "ACCgGccaaaaGGAaacaaggCcGGAuuuaAgaCgcgGAUgcACUGCugcGuGUACUguaGaGuCuGGCGGAUGUCGACaGaCuCuauUUUUUUAU", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [[0, 33, 34, 96], [0, 33, 34, 96], [0, 33, 34, 96], [0, 33, 33, 95]] ), ) ) self.assertEqual( str(alignment), """\ CP000036. 0 ACCGGCGCAGAGGAGACAAUGCCGGACUUAAGACGCGGAUGCACUGCUGUGUGUACUGUA U00096.3/ 0 ACCGGCGCAGAGGAGACAAUGCCGGAUUUAAGACGCGGAUGCACUGCUGUGUGUACUGUA CP000034. 0 ACCGGUCACCAGGACCCCAGGCCGGAUUUAAGACGAGGAUGCACUGCUGUGUGUACUGUA CP011132. 0 ACCCGCCACACGGAAUAAUAACGGGAACACAUG-AAGGAUAAACUGCUGUGUGUACUGUA CP000036. 60 GAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU 96 U00096.3/ 60 GAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU 96 CP000034. 60 GAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU 96 CP011132. 59 GAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU 95 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID McaS #=GF AC RF00115 #=GF DE McaS/IsrA RNA #=GF AU Argasinska J; 0000-0003-2678-2824 #=GF SE Argasinska J #=GF SS Predicted; 22289118 #=GF GA 42.00 #=GF TC 42.10 #=GF NC 38.70 #=GF BM cmbuild -n -F CM SEED #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize 128 CM SEQDB #=GF TP Gene; sRNA; #=GF PI IS061; #=GF CL CL00106 #=GF WK IS061_RNA #=GF CB cmcalibrate --mpi CM #=GF RN [1] #=GF RM 12069726 #=GF RT A bioinformatics based approach to discover small RNA genes in the #=GF RT Escherichia coli genome. #=GF RA Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB #=GF RL Biosystems 2002;65:157-177. #=GF RN [2] #=GF RM 23666921 #=GF RT Dual function of the McaS small RNA in controlling biofilm formation. #=GF RA Jorgensen MG, Thomason MK, Havelund J, Valentin-Hansen P, Storz G #=GF RL Genes Dev. 2013;27:1132-1145. #=GF RN [3] #=GF RM 22289118 #=GF RT A small RNA that regulates motility and biofilm formation in response #=GF RT to changes in nutrient availability in Escherichia coli. #=GF RA Thomason MK, Fontaine F, De Lay N, Storz G #=GF RL Mol Microbiol. 2012;84:17-35. #=GF RN [4] #=GF RM 26609136 #=GF RT Ribonucleoprotein particles of bacterial small non-coding RNA IsrA #=GF RT (IS61 or McaS) and its interaction with RNA polymerase core may link #=GF RT transcription to mRNA fate. #=GF RA van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N #=GF RL Nucleic Acids Res. 2016;44:2577-2592. #=GF DR SO; 0001263; ncRNA_gene; #=GF DR GO; 0005515; protein binding; #=GF DR GO; 0006417; regulation of translation; #=GF CC This family consists of several bacterial RNA genes which are found #=GF CC between the abgR and ydaL genes in Escherichia coli and Shigella #=GF CC flexneri.[1] It was discovered using a computational screen of the E. #=GF CC coli genome.[1] Subsequent characterisation of ISO61 region has #=GF CC revealed that the reverse strand is actually a CsrA binding ncRNA #=GF CC called McaS and that it has a role in biofilm formation control.[2] #=GF CC Furthermore, it has been shown that McaS(IsrA) exists as a #=GF CC ribonucleoprotein particles (sRNPs), which involve a defined set of #=GF CC proteins including Hfq, S1, CsrA, ProQ and PNPase.[4] #=GF SQ 4 CP000036.1/1703842-1703937 ACCGGCGCAGAGGAGACAAUGCCGGACUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU U00096.3/1405751-1405656 ACCGGCGCAGAGGAGACAAUGCCGGAUUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU CP000034.1/1309299-1309204 ACCGGUCACCAGGACCCCAGGCCGGAUUUAAGACGAGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU CP011132.1/1732716-1732810 ACCCGCCACACGGAAUAAUAACGGGAACACAUG-AAGGAUAAACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU #=GC SS_cons :<<<<<<____________>>>>>>,,,,,,,<<<<<<________>>>>>>-----<<<<<<<<<<-<<_____>>->>>>>>>>>>:::::::: #=GC RF ACCgGccaaaaGGAaacaaggCcGGAuuuaAgaCgcgGAUgcACUGCugcGuGUACUguaGaGuCuGGCGGAUGUCGACaGaCuCuauUUUUUUAU // """, ) def check_alignment_rfam4(self, alignment): """Check the alignment obtained by parsing Rfam record IRES_KSHV.""" self.assertEqual(alignment.annotations["accession"], "RF00511") self.assertEqual(alignment.annotations["identifier"], "IRES_KSHV") self.assertEqual( alignment.annotations["definition"], "Kaposi's sarcoma-associated herpesvirus internal ribosome entry site", ) self.assertEqual( alignment.annotations["author"], ["Moxon SJ; 0000-0003-4644-1816"] ) self.assertEqual( alignment.annotations["source of seed"], "Published; 11160685, INFERNAL" ) self.assertEqual( alignment.annotations["source of structure"], "Published; PMID:11160685" ) self.assertEqual(alignment.annotations["gathering method"], "100.00") self.assertEqual(alignment.annotations["trusted cutoff"], "317.10") self.assertEqual(alignment.annotations["noise cutoff"], "30.10") self.assertEqual(alignment.annotations["type"], "Cis-reg; IRES;") self.assertEqual(alignment.annotations["build method"], "cmbuild -F CM SEED") self.assertEqual( alignment.annotations["calibration method"], "cmcalibrate --mpi CM" ) self.assertEqual( alignment.annotations["search method"], "cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB", ) self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0], {"reference": "SO; 0000243; internal_ribosome_entry_site;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "GO; 0043022; ribosome binding;"}, ) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "11160685") self.assertEqual( alignment.annotations["references"][0]["title"], "Kaposi's sarcoma-associated herpesvirus vCyclin open reading frame contains an internal ribosome entry site.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Bieleski L, Talbot SJ" ) self.assertEqual( alignment.annotations["references"][0]["location"], "J Virol 2001;75:1864-1869.", ) self.assertEqual(alignment.annotations["references"][1]["number"], 2) self.assertEqual(alignment.annotations["references"][1]["medline"], "14993645") self.assertEqual( alignment.annotations["references"][1]["title"], "A polypyrimidine tract facilitates the expression of Kaposi's sarcoma-associated herpesvirus vFLIP through an internal ribosome entry site.", ) self.assertEqual( alignment.annotations["references"][1]["author"], "Bieleski L, Hindley C, Talbot SJ", ) self.assertEqual( alignment.annotations["references"][1]["location"], "J Gen Virol 2004;85:615-620.", ) self.assertEqual( alignment.annotations["comment"], "This family represents the Kaposi's sarcoma-associated herpesvirus (KSHV) internal ribosome entry site (IRES) present in the vCyclin gene. The vCyclin and vFLIP coding sequences are present on a bicistronic transcript and it is thought the IRES may initiate translation of vFLIP from this bicistronic transcript [1,2].", ) self.assertEqual( alignment.annotations["wikipedia"], [ "Kaposi's_sarcoma-associated_herpesvirus_internal_ribosome_entry_site_(IRES)" ], ) self.assertEqual(len(alignment.sequences), 5) self.assertEqual(alignment.sequences[0].id, "AF148805.2/123462-123215") self.assertEqual(alignment.sequences[1].id, "U40667.1/2005-2252") self.assertEqual(alignment.sequences[2].id, "U79416.1/354-601") self.assertEqual(alignment.sequences[3].id, "U93872.2/123729-123482") self.assertEqual(alignment.sequences[4].id, "U75698.1/123214-122967") self.assertEqual( alignment.sequences[0].seq, "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment.sequences[1].seq, "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment.sequences[2].seq, "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment.sequences[3].seq, "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment.sequences[4].seq, "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment[0], "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment[1], "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment[2], "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment[3], "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment[4], "UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG", ) self.assertEqual( alignment.column_annotations["consensus secondary structure"], ":::::::::<<<---<<<<<<<<<<---<<<<<--<<<<<-------<<<<<______>>>>>---->>>>>---->>>>>--->>>>>->>>>>-->>>,,<<<_______>>>-----------------((((((((((,,,<<<<----<<-<<<<<<------<<-<<<____>>>->>---->>>>>>>>--->>>>,,,,,,,,,,,<<<_____>>>,))))))-----)))):::::::", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "UUGCUAUGCCGCGGCaGaCuCCucuUCCCGCCaAGaaCuuAUAGACCaGGaGAAAGAACuCCuUGAGaaGuuGGCGuGGCGAACagaGGCaGuCuUAGCGACGGaCGUaACUuCCUUCUUGUUACUUAAAUUGcuGgGgGGCUCCCaaCACCUGGACuuuuGGCACCACgAGGuCaACaCCCcGAUUACaaaaGCCUUAGuuGACCCAAAGACUGGcUCAUUgCCCGCCcCcAUUAUCagCGCUGCAG", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 248], [0, 248], [0, 248], [0, 248], [0, 248]]), ) ) self.assertEqual( str(alignment), """\ AF148805. 0 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACU U40667.1/ 0 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACU U79416.1/ 0 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACU U93872.2/ 0 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACU U75698.1/ 0 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACU AF148805. 60 CCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUU U40667.1/ 60 CCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUU U79416.1/ 60 CCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUU U93872.2/ 60 CCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUU U75698.1/ 60 CCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUU AF148805. 120 GUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACAC U40667.1/ 120 GUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACAC U79416.1/ 120 GUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACAC U93872.2/ 120 GUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACAC U75698.1/ 120 GUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACAC AF148805. 180 CCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAG U40667.1/ 180 CCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAG U79416.1/ 180 CCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAG U93872.2/ 180 CCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAG U75698.1/ 180 CCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAG AF148805. 240 CGCUGCAG 248 U40667.1/ 240 CGCUGCAG 248 U79416.1/ 240 CGCUGCAG 248 U93872.2/ 240 CGCUGCAG 248 U75698.1/ 240 CGCUGCAG 248 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID IRES_KSHV #=GF AC RF00511 #=GF DE Kaposi's sarcoma-associated herpesvirus internal ribosome entry site #=GF AU Moxon SJ; 0000-0003-4644-1816 #=GF SE Published; 11160685, INFERNAL #=GF SS Published; PMID:11160685 #=GF GA 100.00 #=GF TC 317.10 #=GF NC 30.10 #=GF BM cmbuild -F CM SEED #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB #=GF TP Cis-reg; IRES; #=GF WK Kaposi's_sarcoma-associated_herpesvirus_internal_ribosome_entry_site_(IRES) #=GF CB cmcalibrate --mpi CM #=GF RN [1] #=GF RM 11160685 #=GF RT Kaposi's sarcoma-associated herpesvirus vCyclin open reading frame #=GF RT contains an internal ribosome entry site. #=GF RA Bieleski L, Talbot SJ #=GF RL J Virol 2001;75:1864-1869. #=GF RN [2] #=GF RM 14993645 #=GF RT A polypyrimidine tract facilitates the expression of Kaposi's #=GF RT sarcoma-associated herpesvirus vFLIP through an internal ribosome #=GF RT entry site. #=GF RA Bieleski L, Hindley C, Talbot SJ #=GF RL J Gen Virol 2004;85:615-620. #=GF DR SO; 0000243; internal_ribosome_entry_site; #=GF DR GO; 0043022; ribosome binding; #=GF CC This family represents the Kaposi's sarcoma-associated herpesvirus #=GF CC (KSHV) internal ribosome entry site (IRES) present in the vCyclin #=GF CC gene. The vCyclin and vFLIP coding sequences are present on a #=GF CC bicistronic transcript and it is thought the IRES may initiate #=GF CC translation of vFLIP from this bicistronic transcript [1,2]. #=GF SQ 5 AF148805.2/123462-123215 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG U40667.1/2005-2252 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG U79416.1/354-601 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG U93872.2/123729-123482 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG U75698.1/123214-122967 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG #=GC SS_cons :::::::::<<<---<<<<<<<<<<---<<<<<--<<<<<-------<<<<<______>>>>>---->>>>>---->>>>>--->>>>>->>>>>-->>>,,<<<_______>>>-----------------((((((((((,,,<<<<----<<-<<<<<<------<<-<<<____>>>->>---->>>>>>>>--->>>>,,,,,,,,,,,<<<_____>>>,))))))-----))))::::::: #=GC RF UUGCUAUGCCGCGGCaGaCuCCucuUCCCGCCaAGaaCuuAUAGACCaGGaGAAAGAACuCCuUGAGaaGuuGGCGuGGCGAACagaGGCaGuCuUAGCGACGGaCGUaACUuCCUUCUUGUUACUUAAAUUGcuGgGgGGCUCCCaaCACCUGGACuuuuGGCACCACgAGGuCaACaCCCcGAUUACaaaaGCCUUAGuuGACCCAAAGACUGGcUCAUUgCCCGCCcCcAUUAUCagCGCUGCAG // """, ) def check_alignment_rfam5(self, alignment): """Check the alignment obtained by parsing Rfam record BMV3_UPD-PK3.""" self.assertEqual(alignment.annotations["accession"], "RF01113") self.assertEqual(alignment.annotations["identifier"], "BMV3_UPD-PK3") self.assertEqual( alignment.annotations["definition"], "Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR", ) self.assertEqual( alignment.annotations["author"], ["Wilkinson A; 0000-0001-7406-0151"] ) self.assertEqual(alignment.annotations["source of seed"], "Pseudobase") self.assertEqual(alignment.annotations["source of structure"], "Pseudobase") self.assertEqual(alignment.annotations["gathering method"], "36.00") self.assertEqual(alignment.annotations["trusted cutoff"], "37.00") self.assertEqual(alignment.annotations["noise cutoff"], "33.30") self.assertEqual(alignment.annotations["type"], "Cis-reg;") self.assertEqual(alignment.annotations["build method"], "cmbuild -F CM SEED") self.assertEqual( alignment.annotations["calibration method"], "cmcalibrate --mpi CM" ) self.assertEqual( alignment.annotations["search method"], "cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB", ) self.assertEqual(len(alignment.annotations["database references"]), 4) self.assertEqual( alignment.annotations["database references"][0], {"reference": "PKBASE; PKB00156;"}, ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "SO; 0005836; regulatory_region;"}, ) self.assertEqual( alignment.annotations["database references"][2], {"reference": "GO; 1904973; positive regulation of viral translation;"}, ) self.assertEqual( alignment.annotations["database references"][3], {"reference": "GO; 0046782; regulation of viral transcription;"}, ) self.assertEqual(len(alignment.annotations["references"]), 1) self.assertEqual(alignment.annotations["references"][0]["number"], 1) self.assertEqual(alignment.annotations["references"][0]["medline"], "7684465") self.assertEqual( alignment.annotations["references"][0]["title"], "Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to replication and translation.", ) self.assertEqual( alignment.annotations["references"][0]["author"], "Lahser FC, Marsh LE, Hall TC", ) self.assertEqual( alignment.annotations["references"][0]["location"], "J Virol. 1993;67:3295-3303.", ) self.assertEqual(alignment.annotations["wikipedia"], ["UPSK_RNA"]) self.assertEqual( alignment.annotations["**"], "seedtax: Viruses; unclassified sequences" ) self.assertEqual(len(alignment.sequences), 2) self.assertEqual(alignment.sequences[0].id, "X01678.1/2648-2670") self.assertEqual(alignment.sequences[1].id, "X58459.1/659-681") self.assertEqual(alignment.sequences[0].seq, "ACUUUGGCUAAGUUUAAAAGCUU") self.assertEqual(alignment.sequences[1].seq, "ACUUUGGCUAAGGUUAAAAGCUU") self.assertEqual(alignment[0], "ACUUUGGCUAAGUUUAAAAGCUU") self.assertEqual(alignment[1], "ACUUUGGCUAAGGUUAAAAGCUU") self.assertEqual( alignment.column_annotations["consensus secondary structure"], ":<<<_AAAA>>>::::::aaaa:", ) self.assertEqual( alignment.column_annotations["reference coordinate annotation"], "ACUUUGGCUAAGuUUAAAAGCUU", ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 23], [0, 23]])) ) self.assertEqual( str(alignment), """\ X01678.1/ 0 ACUUUGGCUAAGUUUAAAAGCUU 23 0 ||||||||||||.|||||||||| 23 X58459.1/ 0 ACUUUGGCUAAGGUUAAAAGCUU 23 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID BMV3_UPD-PK3 #=GF AC RF01113 #=GF DE Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR #=GF AU Wilkinson A; 0000-0001-7406-0151 #=GF SE Pseudobase #=GF SS Pseudobase #=GF GA 36.00 #=GF TC 37.00 #=GF NC 33.30 #=GF BM cmbuild -F CM SEED #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB #=GF TP Cis-reg; #=GF WK UPSK_RNA #=GF CB cmcalibrate --mpi CM #=GF ** seedtax: Viruses; unclassified sequences #=GF RN [1] #=GF RM 7684465 #=GF RT Contributions of the brome mosaic virus RNA-3 3'-nontranslated region #=GF RT to replication and translation. #=GF RA Lahser FC, Marsh LE, Hall TC #=GF RL J Virol. 1993;67:3295-3303. #=GF DR PKBASE; PKB00156; #=GF DR SO; 0005836; regulatory_region; #=GF DR GO; 1904973; positive regulation of viral translation; #=GF DR GO; 0046782; regulation of viral transcription; #=GF SQ 2 X01678.1/2648-2670 ACUUUGGCUAAGUUUAAAAGCUU X58459.1/659-681 ACUUUGGCUAAGGUUAAAAGCUU #=GC SS_cons :<<<_AAAA>>>::::::aaaa: #=GC RF ACUUUGGCUAAGuUUAAAAGCUU // """, ) def check_alignment_cath1(self, alignment): """Check the alignment obtained by parsing CATH record 3.30.160.60/FF/004774.""" self.assertEqual(alignment.annotations["identifier"], "3.30.160.60/FF/004774") self.assertEqual(alignment.annotations["definition"], "Uncharacterized protein") self.assertEqual(alignment.annotations["accession"], "3.30.160.60/FF/004774") self.assertEqual(alignment.annotations["type"], "FunFam") self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0], {"reference": "CATH: v4.3"} ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "DOPS: 0.000"}, ) self.assertEqual(len(alignment.sequences), 1) self.assertEqual(alignment.sequences[0].annotations["accession"], "L7MZX4") self.assertEqual( alignment.sequences[0].annotations["organism"], "Anolis carolinensis" ) self.assertEqual(alignment.sequences[0].description, "Uncharacterized protein") self.assertEqual(len(alignment.sequences[0].dbxrefs), 1) self.assertEqual( alignment.sequences[0].dbxrefs[0], "ORG; Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Lepidosauria; Squamata; Iguania; Dactyloidae; Anolis; Anolis carolinensis;", ) self.assertEqual(alignment.sequences[0].id, "L7MZX4/382-398") self.assertEqual(alignment.sequences[0].seq, "GEKPYECLECGKRFTAR") self.assertEqual(alignment[0], "GEKPYECLECGKRFTAR") self.assertEqual( alignment.column_annotations["consensus score"], "00000000000000000" ) self.assertEqual( alignment.column_annotations["consensus score 70"], "_________________" ) self.assertEqual( alignment.column_annotations["consensus score 80"], "_________________" ) self.assertEqual( alignment.column_annotations["consensus score 90"], "_________________" ) self.assertTrue(np.array_equal(alignment.coordinates, np.array([[0, 17]]))) self.assertEqual( str(alignment), """\ L7MZX4/38 0 GEKPYECLECGKRFTAR 17 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 3.30.160.60/FF/004774 #=GF AC 3.30.160.60/FF/004774 #=GF DE Uncharacterized protein #=GF TP FunFam #=GF DR CATH: v4.3 #=GF DR DOPS: 0.000 #=GF SQ 1 #=GS L7MZX4/382-398 AC L7MZX4 #=GS L7MZX4/382-398 OS Anolis carolinensis #=GS L7MZX4/382-398 DE Uncharacterized protein #=GS L7MZX4/382-398 DR ORG; Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Lepidosauria; Squamata; Iguania; Dactyloidae; Anolis; Anolis carolinensis; L7MZX4/382-398 GEKPYECLECGKRFTAR #=GC scorecons 00000000000000000 #=GC scorecons_70 _________________ #=GC scorecons_80 _________________ #=GC scorecons_90 _________________ // """, ) def check_alignment_cath2(self, alignment): """Check the alignment obtained by parsing CATH record 2.105.10.10/FF/000002.""" self.assertEqual(alignment.annotations["identifier"], "2.105.10.10/FF/000002") self.assertEqual(alignment.annotations["definition"], "Adsorption protein P2") self.assertEqual(alignment.annotations["accession"], "2.105.10.10/FF/000002") self.assertEqual(alignment.annotations["type"], "FunFam") self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0], {"reference": "CATH: v4.3"} ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "DOPS: 0.000"}, ) self.assertEqual(alignment.sequences[0].annotations["accession"], "P27378") self.assertEqual(alignment.sequences[0].annotations["organism"], "") self.assertEqual(alignment.sequences[0].description, "Adsorption protein P2") self.assertEqual(len(alignment.sequences[0].dbxrefs), 2) self.assertEqual(alignment.sequences[0].dbxrefs[0], "ORG;") self.assertEqual(alignment.sequences[0].dbxrefs[1], "GO; GO:0019012;") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(alignment.sequences[0].id, "P27378/2-64") self.assertEqual( alignment.sequences[0].seq, "ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDSSNR", ) self.assertEqual( alignment[0], "ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDSSNR", ) self.assertEqual( alignment.column_annotations["consensus score"], "000000000000000000000000000000000000000000000000000000000000000", ) self.assertEqual( alignment.column_annotations["consensus score 70"], "_______________________________________________________________", ) self.assertEqual( alignment.column_annotations["consensus score 80"], "_______________________________________________________________", ) self.assertEqual( alignment.column_annotations["consensus score 90"], "_______________________________________________________________", ) self.assertTrue(np.array_equal(alignment.coordinates, np.array([[0, 63]]))) self.assertEqual( str(alignment), """\ P27378/2- 0 ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDS P27378/2- 60 SNR 63 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 2.105.10.10/FF/000002 #=GF AC 2.105.10.10/FF/000002 #=GF DE Adsorption protein P2 #=GF TP FunFam #=GF DR CATH: v4.3 #=GF DR DOPS: 0.000 #=GF SQ 1 #=GS P27378/2-64 AC P27378 #=GS P27378/2-64 OS #=GS P27378/2-64 DE Adsorption protein P2 #=GS P27378/2-64 DR ORG; #=GS P27378/2-64 DR GO; GO:0019012; P27378/2-64 ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDSSNR #=GC scorecons 000000000000000000000000000000000000000000000000000000000000000 #=GC scorecons_70 _______________________________________________________________ #=GC scorecons_80 _______________________________________________________________ #=GC scorecons_90 _______________________________________________________________ // """, ) def check_alignment_cath3(self, alignment): """Check the alignment obtained by parsing CATH record 1.10.275.10/FF/000026.""" self.assertEqual(alignment.annotations["identifier"], "1.10.275.10/FF/000026") self.assertEqual(alignment.annotations["definition"], "Adenylosuccinate lyase") self.assertEqual(alignment.annotations["accession"], "1.10.275.10/FF/000026") self.assertEqual(alignment.annotations["type"], "FunFam") self.assertEqual(len(alignment.annotations["database references"]), 2) self.assertEqual( alignment.annotations["database references"][0], {"reference": "CATH: v4.3"} ) self.assertEqual( alignment.annotations["database references"][1], {"reference": "DOPS: 0.000"}, ) self.assertEqual(alignment.sequences[0].annotations["accession"], "Q9X0I0") self.assertEqual( alignment.sequences[0].annotations["organism"], "Thermotoga maritima MSB8" ) self.assertEqual(alignment.sequences[0].description, "Adenylosuccinate lyase") self.assertEqual(len(alignment.sequences[0].dbxrefs), 3) self.assertEqual(alignment.sequences[0].dbxrefs[0], "CATH; 1c3c; B:2-92;") self.assertEqual( alignment.sequences[0].dbxrefs[1], "ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima;", ) self.assertEqual(alignment.sequences[0].dbxrefs[2], "EC; 4.3.2.2;") self.assertEqual(alignment.sequences[1].annotations["accession"], "Q9X0I0") self.assertEqual( alignment.sequences[1].annotations["organism"], "Thermotoga maritima MSB8" ) self.assertEqual(alignment.sequences[1].description, "Adenylosuccinate lyase") self.assertEqual(len(alignment.sequences[1].dbxrefs), 3) self.assertEqual(alignment.sequences[1].dbxrefs[0], "CATH; 1c3c; A:2-92;") self.assertEqual( alignment.sequences[1].dbxrefs[1], "ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima;", ) self.assertEqual(alignment.sequences[1].dbxrefs[2], "EC; 4.3.2.2;") self.assertEqual(alignment.sequences[2].annotations["accession"], "Q9X0I0") self.assertEqual( alignment.sequences[2].annotations["organism"], "Thermotoga maritima MSB8" ) self.assertEqual(alignment.sequences[2].description, "Adenylosuccinate lyase") self.assertEqual(len(alignment.sequences[2].dbxrefs), 2) self.assertEqual( alignment.sequences[2].dbxrefs[0], "ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima;", ) self.assertEqual(alignment.sequences[2].dbxrefs[1], "EC; 4.3.2.2;") self.assertEqual(alignment.sequences[3].annotations["accession"], "G4FEQ2") self.assertEqual( alignment.sequences[3].annotations["organism"], "Thermotoga maritima MSB8" ) self.assertEqual(alignment.sequences[3].description, "Adenylosuccinate lyase") self.assertEqual(len(alignment.sequences[3].dbxrefs), 2) self.assertEqual( alignment.sequences[3].dbxrefs[0], "ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima;", ) self.assertEqual(alignment.sequences[3].dbxrefs[1], "EC; 4.3.2.2;") self.assertEqual(len(alignment.sequences), 4) self.assertEqual(alignment.sequences[0].id, "1c3cB01/1-91") self.assertEqual(alignment.sequences[1].id, "1c3cA01/1-91") self.assertEqual(alignment.sequences[2].id, "Q9X0I0/2-92") self.assertEqual(alignment.sequences[3].id, "G4FEQ2/2-92") self.assertEqual( alignment.sequences[0].seq, "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment.sequences[1].seq, "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment.sequences[2].seq, "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment.sequences[3].seq, "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment[0], "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment[1], "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment[2], "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment[3], "VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL", ) self.assertEqual( alignment.sequences[0].letter_annotations["Catalytic Site Atlas"], "__________________________________________________________________0________________________", ) self.assertEqual( alignment.column_annotations["consensus score"], "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000", ) self.assertEqual( alignment.column_annotations["consensus score 70"], "___________________________________________________________________________________________", ) self.assertEqual( alignment.column_annotations["consensus score 80"], "___________________________________________________________________________________________", ) self.assertEqual( alignment.column_annotations["consensus score 90"], "___________________________________________________________________________________________", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 91], [0, 91], [0, 91], [0, 91]]) ) ) self.assertEqual( str(alignment), """\ 1c3cB01/1 0 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKK 1c3cA01/1 0 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKK Q9X0I0/2- 0 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKK G4FEQ2/2- 0 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKK 1c3cB01/1 60 IEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL 91 1c3cA01/1 60 IEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL 91 Q9X0I0/2- 60 IEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL 91 G4FEQ2/2- 60 IEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL 91 """, ) self.assertEqual( format(alignment, "stockholm"), """\ # STOCKHOLM 1.0 #=GF ID 1.10.275.10/FF/000026 #=GF AC 1.10.275.10/FF/000026 #=GF DE Adenylosuccinate lyase #=GF TP FunFam #=GF DR CATH: v4.3 #=GF DR DOPS: 0.000 #=GF SQ 4 #=GS 1c3cB01/1-91 AC Q9X0I0 #=GS 1c3cB01/1-91 OS Thermotoga maritima MSB8 #=GS 1c3cB01/1-91 DE Adenylosuccinate lyase #=GS 1c3cB01/1-91 DR CATH; 1c3c; B:2-92; #=GS 1c3cB01/1-91 DR ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima; #=GS 1c3cB01/1-91 DR EC; 4.3.2.2; #=GS 1c3cA01/1-91 AC Q9X0I0 #=GS 1c3cA01/1-91 OS Thermotoga maritima MSB8 #=GS 1c3cA01/1-91 DE Adenylosuccinate lyase #=GS 1c3cA01/1-91 DR CATH; 1c3c; A:2-92; #=GS 1c3cA01/1-91 DR ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima; #=GS 1c3cA01/1-91 DR EC; 4.3.2.2; #=GS Q9X0I0/2-92 AC Q9X0I0 #=GS Q9X0I0/2-92 OS Thermotoga maritima MSB8 #=GS Q9X0I0/2-92 DE Adenylosuccinate lyase #=GS Q9X0I0/2-92 DR ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima; #=GS Q9X0I0/2-92 DR EC; 4.3.2.2; #=GS G4FEQ2/2-92 AC G4FEQ2 #=GS G4FEQ2/2-92 OS Thermotoga maritima MSB8 #=GS G4FEQ2/2-92 DE Adenylosuccinate lyase #=GS G4FEQ2/2-92 DR ORG; Bacteria; Thermotogae; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga; Thermotoga maritima; #=GS G4FEQ2/2-92 DR EC; 4.3.2.2; 1c3cB01/1-91 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL #=GR 1c3cB01/1-91 CSA __________________________________________________________________0________________________ 1c3cA01/1-91 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL Q9X0I0/2-92 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL G4FEQ2/2-92 VERYSLSPMKDLWTEEAKYRRWLEVELAVTRAYEELGMIPKGVTERIRNNAKIDVELFKKIEEKTNHDVVAFVEGIGSMIGEDSRFFHYGL #=GC scorecons 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 #=GC scorecons_70 ___________________________________________________________________________________________ #=GC scorecons_80 ___________________________________________________________________________________________ #=GC scorecons_90 ___________________________________________________________________________________________ // """, ) def test_reading_writing_alignments_globins45(self): """Test parsing hmmalign output.""" # File generated by running # hmmalign -o globins45.ali globins4.hmm globins45.fa # in the HMMER 3.3.2 tutorial path = "Stockholm/globins45.ali" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_globins45(alignment) alignments = iter(alignments) alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) with Align.parse(path, "stockholm") as alignments: alignment = next(alignments) self.check_alignment_globins45(alignment) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "stockholm") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_alignment_globins45(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_globins45(alignment) def test_reading_writing_alignments_pfam1(self): """Test parsing Pfam record 120_Rick_ant.""" path = "Stockholm/pfam1.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'A', 'E', 'Q', 'I', 'A', 'K', 'E', '-', '-', '-', '-', '-', 'E', 'D', 'D', 'R', 'K', 'F', 'R', 'A', 'F', 'L', 'S', 'N', 'Q', 'D', 'N', 'Y', 'A', 'L', 'I', 'N', 'K', 'A', 'F', 'E', 'D', 'T', 'K', 'T', 'K', 'K', 'N', 'L', 'E', 'K', 'A', 'E', 'I', 'V', 'G', 'Y', 'K', 'N', 'V', 'L', 'S', 'T', 'Y', 'S', 'V', 'A', 'N', 'G', 'Y', 'Q', 'G', 'G', 'F', 'Q', 'P', 'V', 'Q', 'W', 'E', 'N', 'Q', 'V', 'S', 'A', 'S', 'D', 'L', 'R', 'S', 'T', 'V', 'V', 'K', 'N', 'D', 'E', 'G', 'E', 'E', 'L', 'C', 'T', 'L', 'N', 'E', 'T', 'T', 'V', 'K', 'T', 'K', 'D', 'L', 'I', 'V', 'A', 'K', 'Q', 'D', 'G', 'T', 'Q', 'V', 'Q', 'I', 'N', 'S', 'Y', 'R', 'E', 'I', 'N', 'F', 'P', 'I', 'K', 'L', 'D', 'K', 'A', 'N', 'G', 'S', 'M', 'H', 'L', 'S', 'M', 'V', 'A', 'L', 'K', 'A', 'D', 'G', 'T', 'K', 'P', 'A', 'K', 'D', 'K', 'A', 'V', 'Y', 'F', 'T', 'A', 'H', 'Y', 'E', 'E', 'G', 'P', 'N', 'G', 'K', 'P', 'Q', 'L', 'K', 'E', 'I', 'S', 'S', 'P', 'Q', 'P', 'L', 'K', 'F', 'V', 'G', 'T', 'G', 'D', 'D', 'A', 'V', 'A', 'Y', 'I', 'E', 'H', 'G', 'G', 'E', 'I', 'Y', 'T', 'L', 'A', 'V', 'T', 'R', 'G', 'K', 'Y', 'K', 'E', 'M', 'M', 'K', 'E', 'V', 'A', 'L', 'N', 'H', 'G', 'Q', 'S', 'V', 'A', 'L', 'S', 'Q', 'T', 'I', 'A', 'E', 'D', 'L'], ['L', 'A', 'E', 'Q', 'K', 'R', 'K', 'E', 'I', 'E', 'E', 'E', 'K', 'E', 'K', 'D', 'K', 'T', 'L', 'S', 'T', 'F', 'F', 'G', 'N', 'P', 'A', 'N', 'R', 'E', 'F', 'I', 'D', 'K', 'A', 'L', 'E', 'N', 'P', 'E', 'L', 'K', 'K', 'K', 'L', 'E', 'S', 'I', 'E', 'I', 'A', 'G', 'Y', 'K', 'N', 'V', 'H', 'N', 'T', 'F', 'S', 'A', 'A', 'S', 'G', 'Y', 'P', 'G', 'G', 'F', 'K', 'P', 'V', 'Q', 'W', 'E', 'N', 'Q', 'V', 'S', 'A', 'N', 'D', 'L', 'R', 'A', 'T', 'V', 'V', 'K', 'N', 'D', 'A', 'G', 'D', 'E', 'L', 'C', 'T', 'L', 'N', 'E', 'T', 'T', 'V', 'K', 'T', 'K', 'P', 'F', 'T', 'V', 'A', 'K', 'Q', 'D', 'G', 'T', 'Q', 'V', 'Q', 'I', 'S', 'S', 'Y', 'R', 'E', 'I', 'D', 'F', 'P', 'I', 'K', 'L', 'D', 'K', 'A', 'D', 'G', 'S', 'M', 'H', 'L', 'S', 'M', 'V', 'A', 'L', 'K', 'A', 'D', 'G', 'T', 'K', 'P', 'S', 'K', 'D', 'K', 'A', 'V', 'Y', 'F', 'T', 'A', 'H', 'Y', 'E', 'E', 'G', 'P', 'N', 'G', 'K', 'P', 'Q', 'L', 'K', 'E', 'I', 'S', 'S', 'P', 'K', 'P', 'L', 'K', 'F', 'A', 'G', 'T', 'G', 'D', 'D', 'A', 'I', 'A', 'Y', 'I', 'E', 'H', 'G', 'G', 'E', 'I', 'Y', 'T', 'L', 'A', 'V', 'T', 'R', 'G', 'K', 'Y', 'K', 'E', 'M', 'M', 'K', 'E', 'V', 'E', 'L', 'N', 'Q', 'G', 'Q', 'S', 'V', 'D', 'L', 'S', 'Q', '-', '-', 'A', 'E', 'D', 'I']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam1(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'A', 'E', 'Q', 'I', 'A', 'K', 'E', '-', '-', '-', '-', '-', 'E', 'D', 'D', 'R', 'K', 'F', 'R', 'A', 'F', 'L', 'S', 'N', 'Q', 'D', 'N', 'Y', 'A', 'L', 'I', 'N', 'K', 'A', 'F', 'E', 'D', 'T', 'K', 'T', 'K', 'K', 'N', 'L', 'E', 'K', 'A', 'E', 'I', 'V', 'G', 'Y', 'K', 'N', 'V', 'L', 'S', 'T', 'Y', 'S', 'V', 'A', 'N', 'G', 'Y', 'Q', 'G', 'G', 'F', 'Q', 'P', 'V', 'Q', 'W', 'E', 'N', 'Q', 'V', 'S', 'A', 'S', 'D', 'L', 'R', 'S', 'T', 'V', 'V', 'K', 'N', 'D', 'E', 'G', 'E', 'E', 'L', 'C', 'T', 'L', 'N', 'E', 'T', 'T', 'V', 'K', 'T', 'K', 'D', 'L', 'I', 'V', 'A', 'K', 'Q', 'D', 'G', 'T', 'Q', 'V', 'Q', 'I', 'N', 'S', 'Y', 'R', 'E', 'I', 'N', 'F', 'P', 'I', 'K', 'L', 'D', 'K', 'A', 'N', 'G', 'S', 'M', 'H', 'L', 'S', 'M', 'V', 'A', 'L', 'K', 'A', 'D', 'G', 'T', 'K', 'P', 'A', 'K', 'D', 'K', 'A', 'V', 'Y', 'F', 'T', 'A', 'H', 'Y', 'E', 'E', 'G', 'P', 'N', 'G', 'K', 'P', 'Q', 'L', 'K', 'E', 'I', 'S', 'S', 'P', 'Q', 'P', 'L', 'K', 'F', 'V', 'G', 'T', 'G', 'D', 'D', 'A', 'V', 'A', 'Y', 'I', 'E', 'H', 'G', 'G', 'E', 'I', 'Y', 'T', 'L', 'A', 'V', 'T', 'R', 'G', 'K', 'Y', 'K', 'E', 'M', 'M', 'K', 'E', 'V', 'A', 'L', 'N', 'H', 'G', 'Q', 'S', 'V', 'A', 'L', 'S', 'Q', 'T', 'I', 'A', 'E', 'D', 'L'], ['L', 'A', 'E', 'Q', 'K', 'R', 'K', 'E', 'I', 'E', 'E', 'E', 'K', 'E', 'K', 'D', 'K', 'T', 'L', 'S', 'T', 'F', 'F', 'G', 'N', 'P', 'A', 'N', 'R', 'E', 'F', 'I', 'D', 'K', 'A', 'L', 'E', 'N', 'P', 'E', 'L', 'K', 'K', 'K', 'L', 'E', 'S', 'I', 'E', 'I', 'A', 'G', 'Y', 'K', 'N', 'V', 'H', 'N', 'T', 'F', 'S', 'A', 'A', 'S', 'G', 'Y', 'P', 'G', 'G', 'F', 'K', 'P', 'V', 'Q', 'W', 'E', 'N', 'Q', 'V', 'S', 'A', 'N', 'D', 'L', 'R', 'A', 'T', 'V', 'V', 'K', 'N', 'D', 'A', 'G', 'D', 'E', 'L', 'C', 'T', 'L', 'N', 'E', 'T', 'T', 'V', 'K', 'T', 'K', 'P', 'F', 'T', 'V', 'A', 'K', 'Q', 'D', 'G', 'T', 'Q', 'V', 'Q', 'I', 'S', 'S', 'Y', 'R', 'E', 'I', 'D', 'F', 'P', 'I', 'K', 'L', 'D', 'K', 'A', 'D', 'G', 'S', 'M', 'H', 'L', 'S', 'M', 'V', 'A', 'L', 'K', 'A', 'D', 'G', 'T', 'K', 'P', 'S', 'K', 'D', 'K', 'A', 'V', 'Y', 'F', 'T', 'A', 'H', 'Y', 'E', 'E', 'G', 'P', 'N', 'G', 'K', 'P', 'Q', 'L', 'K', 'E', 'I', 'S', 'S', 'P', 'K', 'P', 'L', 'K', 'F', 'A', 'G', 'T', 'G', 'D', 'D', 'A', 'I', 'A', 'Y', 'I', 'E', 'H', 'G', 'G', 'E', 'I', 'Y', 'T', 'L', 'A', 'V', 'T', 'R', 'G', 'K', 'Y', 'K', 'E', 'M', 'M', 'K', 'E', 'V', 'E', 'L', 'N', 'Q', 'G', 'Q', 'S', 'V', 'D', 'L', 'S', 'Q', '-', '-', 'A', 'E', 'D', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_pfam1(alignment) def test_reading_writing_alignments_pfam2(self): """Test parsing Pfam record 7kD_DNA_binding.""" path = "Stockholm/pfam2.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'K', 'F', 'K', 'Y', 'K', 'G', 'Q', 'D', 'L', 'E', 'V', 'D', 'I', 'S', 'K', 'V', 'K', 'K', 'V', 'W', 'K', 'V', 'G', 'K', 'M', 'V', 'S', 'F', 'T', 'Y', 'D', 'D', '-', 'N', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'L', 'N', 'M', 'I', 'G', 'K'], ['T', 'V', 'K', 'F', 'K', 'Y', 'K', 'G', 'E', 'E', 'K', 'Q', 'V', 'D', 'I', 'S', 'K', 'I', 'K', 'K', 'V', 'W', 'R', 'V', 'G', 'K', 'M', 'I', 'S', 'F', 'T', 'Y', 'D', 'E', 'G', 'G', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'L', 'Q', 'M', 'L', 'E', 'K'], ['K', 'V', 'R', 'F', 'K', 'Y', 'K', 'G', 'E', 'E', 'K', 'E', 'V', 'D', 'T', 'S', 'K', 'I', 'K', 'K', 'V', 'W', 'R', 'V', 'G', 'K', 'M', 'V', 'S', 'F', 'T', 'Y', 'D', 'D', '-', 'N', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'M', 'D', 'M', 'L', 'A', 'R']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam2(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'K', 'F', 'K', 'Y', 'K', 'G', 'Q', 'D', 'L', 'E', 'V', 'D', 'I', 'S', 'K', 'V', 'K', 'K', 'V', 'W', 'K', 'V', 'G', 'K', 'M', 'V', 'S', 'F', 'T', 'Y', 'D', 'D', '-', 'N', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'L', 'N', 'M', 'I', 'G', 'K'], ['T', 'V', 'K', 'F', 'K', 'Y', 'K', 'G', 'E', 'E', 'K', 'Q', 'V', 'D', 'I', 'S', 'K', 'I', 'K', 'K', 'V', 'W', 'R', 'V', 'G', 'K', 'M', 'I', 'S', 'F', 'T', 'Y', 'D', 'E', 'G', 'G', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'L', 'Q', 'M', 'L', 'E', 'K'], ['K', 'V', 'R', 'F', 'K', 'Y', 'K', 'G', 'E', 'E', 'K', 'E', 'V', 'D', 'T', 'S', 'K', 'I', 'K', 'K', 'V', 'W', 'R', 'V', 'G', 'K', 'M', 'V', 'S', 'F', 'T', 'Y', 'D', 'D', '-', 'N', 'G', 'K', 'T', 'G', 'R', 'G', 'A', 'V', 'S', 'E', 'K', 'D', 'A', 'P', 'K', 'E', 'L', 'M', 'D', 'M', 'L', 'A', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_pfam2(alignment) def test_reading_writing_alignments_pfam3(self): """Test parsing Pfam record 12TM_1.""" path = "Stockholm/pfam3.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam3(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam3(alignment) def test_reading_writing_alignments_pfam4(self): """Test parsing Pfam record 3Beta_HSD.""" path = "Stockholm/pfam4.seed.txt" with open(path, encoding="UTF-8") as stream: # encoding depends on locale by default alignments = Align.parse(stream, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam4(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam4(alignment) def test_reading_writing_alignments_pfam5(self): """Test parsing Pfam record ArsP_1.""" path = "Stockholm/pfam5.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam5(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam5(alignment) def test_reading_writing_alignments_pfam6(self): """Test parsing Pfam record COX2_TM.""" path = "Stockholm/pfam6.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam6(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam6(alignment) def test_reading_writing_alignments_pfam7(self): """Test parsing Pfam record Alpha_E1_glycop.""" path = "Stockholm/pfam7.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam7(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam7(alignment) def test_reading_writing_alignments_pfam8(self): """Test parsing Pfam record Cyclin_N.""" path = "Stockholm/pfam8.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam8(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_pfam8(alignment) def test_reading_writing_alignments_pfam9(self): """Test parsing Pfam record SH3_11.""" path = "Stockholm/pfam9.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'S', 'W', 'S', 'P', 'V', 'V', 'G', 'Q', 'L', 'V', 'Q', 'E', 'R', 'V', 'A', 'R', 'P', 'A', 'S', 'L', 'R', 'P', 'R', 'W', 'H', 'K', 'P', 'S', 'T', 'V', 'L', 'E', 'V', 'L', 'N', 'P', 'R', 'T', 'V', 'V', 'I', 'L', 'D', 'H', 'L', 'G', 'N', 'N', 'R', 'T', 'V', 'S', 'I', 'D', 'N', 'L', 'K', 'P', 'T', 'S', 'H', 'Q']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_pfam9(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'S', 'W', 'S', 'P', 'V', 'V', 'G', 'Q', 'L', 'V', 'Q', 'E', 'R', 'V', 'A', 'R', 'P', 'A', 'S', 'L', 'R', 'P', 'R', 'W', 'H', 'K', 'P', 'S', 'T', 'V', 'L', 'E', 'V', 'L', 'N', 'P', 'R', 'T', 'V', 'V', 'I', 'L', 'D', 'H', 'L', 'G', 'N', 'N', 'R', 'T', 'V', 'S', 'I', 'D', 'N', 'L', 'K', 'P', 'T', 'S', 'H', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_pfam9(alignment) def test_reading_writing_alignments_rfam1(self): """Test parsing Rfam record BTnc005.""" path = "Stockholm/rfam1.seed.txt" with open(path, encoding="UTF-8") as stream: alignments = Align.parse(stream, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'U', 'A', 'A', 'G', 'U', 'A', 'A', 'A', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'A', 'U', 'U', 'G', 'A', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'U', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'A', 'G', 'G', 'A', 'A', 'C', 'C', 'U', 'U', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'U', 'A', 'C', 'U', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'C', 'A', 'G', 'U', 'A', 'A', 'G', 'U', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'U', 'A', 'C', 'A', 'A', 'A', 'U', 'C', 'A', 'G', 'C', '-', 'G', 'A', 'U', 'U', 'U', 'G', 'U', 'A', 'G', 'G', 'U', 'U', 'U', 'U', 'U', 'U'], ['A', 'A', 'A', 'A', 'G', 'U', 'A', 'A', 'G', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'C', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'U', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'U', 'U', 'U', 'G', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'G', 'G', 'G', 'G', 'A', 'G', 'A', 'U', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'U', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'U', 'U', 'G', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'A', '-', '-', 'A', 'G', 'A', '-', 'A', 'A', 'A', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'A', 'A', 'A', 'U', 'U', 'A', 'A', 'U', '-', 'A', 'C', 'U', 'U', 'U', 'A', 'C', 'G', 'G', 'G', 'G', 'A', 'U', 'U', 'U', 'U'], ['G', 'U', 'A', 'A', 'G', 'U', 'A', 'A', 'A', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'A', 'U', 'U', 'G', 'A', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'U', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'A', 'G', 'G', 'A', 'A', 'C', 'C', 'U', 'U', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'U', 'G', 'A', 'A', 'C', 'U', 'A', 'U', 'C', 'C', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'U', 'G', 'A', 'A', 'C', 'A', 'G', 'U', 'C', 'A', 'A', 'A', '-', 'U', 'C', 'C', 'C', 'A', 'C', 'A', 'A', 'A', 'U', 'U', 'C', 'A', 'A', 'U', 'G', 'A', 'U', 'U', 'U', 'G', 'U', 'G', 'G', 'G', 'A', 'C', 'U', 'U', 'U', 'U']], dtype='U') # fmt: on ) ) self.check_alignment_rfam1(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'U', 'A', 'A', 'G', 'U', 'A', 'A', 'A', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'A', 'U', 'U', 'G', 'A', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'U', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'A', 'G', 'G', 'A', 'A', 'C', 'C', 'U', 'U', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'U', 'A', 'C', 'U', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'C', 'A', 'G', 'U', 'A', 'A', 'G', 'U', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'U', 'A', 'C', 'A', 'A', 'A', 'U', 'C', 'A', 'G', 'C', '-', 'G', 'A', 'U', 'U', 'U', 'G', 'U', 'A', 'G', 'G', 'U', 'U', 'U', 'U', 'U', 'U'], ['A', 'A', 'A', 'A', 'G', 'U', 'A', 'A', 'G', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'C', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'U', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'U', 'U', 'U', 'G', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'G', 'G', 'G', 'G', 'A', 'G', 'A', 'U', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'U', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'U', 'U', 'G', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'A', '-', '-', 'A', 'G', 'A', '-', 'A', 'A', 'A', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'A', 'A', 'A', 'U', 'U', 'A', 'A', 'U', '-', 'A', 'C', 'U', 'U', 'U', 'A', 'C', 'G', 'G', 'G', 'G', 'A', 'U', 'U', 'U', 'U'], ['G', 'U', 'A', 'A', 'G', 'U', 'A', 'A', 'A', 'A', 'G', 'U', 'G', 'U', 'A', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'G', 'U', 'U', 'G', 'C', 'A', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'A', 'A', 'U', 'U', 'A', 'U', 'G', 'C', 'G', 'G', 'U', 'G', 'U', 'C', 'A', 'U', 'A', 'G', 'G', 'A', 'A', 'U', 'U', 'G', 'A', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'U', 'G', 'U', 'A', 'A', 'G', 'A', 'U', 'G', 'C', 'U', 'G', 'A', 'U', 'A', 'A', 'U', 'G', 'A', 'G', 'U', 'A', 'A', 'G', 'G', 'A', 'A', 'C', 'C', 'U', 'U', 'A', 'A', 'A', 'G', 'U', 'U', 'A', 'A', 'U', 'C', 'G', 'U', 'U', 'C', 'C', 'C', 'U', 'G', 'U', 'C', 'U', 'C', 'U', 'C', 'C', 'G', 'C', 'U', 'G', 'A', 'A', 'C', 'U', 'A', 'U', 'C', 'C', 'G', 'G', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'U', 'G', 'A', 'A', 'C', 'A', 'G', 'U', 'C', 'A', 'A', 'A', '-', 'U', 'C', 'C', 'C', 'A', 'C', 'A', 'A', 'A', 'U', 'U', 'C', 'A', 'A', 'U', 'G', 'A', 'U', 'U', 'U', 'G', 'U', 'G', 'G', 'G', 'A', 'C', 'U', 'U', 'U', 'U']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_rfam1(alignment) def test_reading_writing_alignments_rfam2(self): """Test parsing Rfam record SraC_RyeA.""" path = "Stockholm/rfam2.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_rfam2(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_rfam2(alignment) def test_reading_writing_alignments_rfam3(self): """Test parsing Rfam record McaS.""" path = "Stockholm/rfam3.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'C', 'G', 'G', 'C', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'A', 'U', 'G', 'C', 'C', 'G', 'G', 'A', 'C', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'A', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'G', 'G', 'C', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'A', 'U', 'G', 'C', 'C', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'A', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'G', 'G', 'U', 'C', 'A', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'C', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'A', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'G', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'C', 'A', 'C', 'G', 'G', 'A', 'A', 'U', 'A', 'A', 'U', 'A', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'U', 'G', '-', 'A', 'A', 'G', 'G', 'A', 'U', 'A', 'A', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'G', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_rfam3(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'C', 'G', 'G', 'C', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'A', 'U', 'G', 'C', 'C', 'G', 'G', 'A', 'C', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'A', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'G', 'G', 'C', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'A', 'U', 'G', 'C', 'C', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'A', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'G', 'G', 'U', 'C', 'A', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'C', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'G', 'G', 'A', 'U', 'U', 'U', 'A', 'A', 'G', 'A', 'C', 'G', 'A', 'G', 'G', 'A', 'U', 'G', 'C', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'G', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U'], ['A', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'C', 'A', 'C', 'G', 'G', 'A', 'A', 'U', 'A', 'A', 'U', 'A', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'U', 'G', '-', 'A', 'A', 'G', 'G', 'A', 'U', 'A', 'A', 'A', 'C', 'U', 'G', 'C', 'U', 'G', 'U', 'G', 'U', 'G', 'U', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'G', 'U', 'C', 'U', 'G', 'G', 'C', 'G', 'G', 'A', 'U', 'G', 'U', 'C', 'G', 'A', 'C', 'A', 'G', 'G', 'C', 'U', 'C', 'U', 'A', 'U', 'U', 'U', 'U', 'U', 'U', 'U', 'A', 'U']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_rfam3(alignment) def test_reading_writing_alignments_rfam4(self): """Test parsing Rfam record IRES_KSHV.""" path = "Stockholm/rfam4.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertRaises(StopIteration, next, alignments) self.check_alignment_rfam4(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.check_alignment_rfam4(alignment) def test_reading_writing_alignments_rfam5(self): """Test parsing Rfam record BMV3_UPD-PK3.""" path = "Stockholm/rfam5.seed.txt" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'U', 'U', 'U', 'G', 'G', 'C', 'U', 'A', 'A', 'G', 'U', 'U', 'U', 'A', 'A', 'A', 'A', 'G', 'C', 'U', 'U'], ['A', 'C', 'U', 'U', 'U', 'G', 'G', 'C', 'U', 'A', 'A', 'G', 'G', 'U', 'U', 'A', 'A', 'A', 'A', 'G', 'C', 'U', 'U']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_rfam5(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'U', 'U', 'U', 'G', 'G', 'C', 'U', 'A', 'A', 'G', 'U', 'U', 'U', 'A', 'A', 'A', 'A', 'G', 'C', 'U', 'U'], ['A', 'C', 'U', 'U', 'U', 'G', 'G', 'C', 'U', 'A', 'A', 'G', 'G', 'U', 'U', 'A', 'A', 'A', 'A', 'G', 'C', 'U', 'U']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_rfam5(alignment) def test_reading_alignments_cath1(self): """Test parsing CATH record 3.30.160.60/FF/004774.""" path = "Stockholm/cath1.sth" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'E', 'K', 'P', 'Y', 'E', 'C', 'L', 'E', 'C', 'G', 'K', 'R', 'F', 'T', 'A', 'R']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_cath1(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'E', 'K', 'P', 'Y', 'E', 'C', 'L', 'E', 'C', 'G', 'K', 'R', 'F', 'T', 'A', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_cath1(alignment) def test_reading_alignments_cath2(self): """Test parsing CATH record 2.105.10.10/FF/000002.""" path = "Stockholm/cath2.sth" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'N', 'F', 'N', 'V', 'P', 'K', 'L', 'G', 'V', 'F', 'P', 'V', 'A', 'A', 'V', 'F', 'D', 'I', 'D', 'N', 'V', 'P', 'E', 'D', 'S', 'S', 'A', 'T', 'G', 'S', 'R', 'W', 'L', 'P', 'S', 'I', 'Y', 'Q', 'G', 'G', 'N', 'Y', 'W', 'G', 'G', 'G', 'P', 'Q', 'A', 'L', 'H', 'A', 'Q', 'V', 'S', 'N', 'F', 'D', 'S', 'S', 'N', 'R']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_cath2(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'N', 'F', 'N', 'V', 'P', 'K', 'L', 'G', 'V', 'F', 'P', 'V', 'A', 'A', 'V', 'F', 'D', 'I', 'D', 'N', 'V', 'P', 'E', 'D', 'S', 'S', 'A', 'T', 'G', 'S', 'R', 'W', 'L', 'P', 'S', 'I', 'Y', 'Q', 'G', 'G', 'N', 'Y', 'W', 'G', 'G', 'G', 'P', 'Q', 'A', 'L', 'H', 'A', 'Q', 'V', 'S', 'N', 'F', 'D', 'S', 'S', 'N', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_cath2(alignment) def test_reading_alignments_cath3(self): """Test parsing CATH record 1.10.275.10/FF/000026.""" path = "Stockholm/cath3.sth" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.check_alignment_cath3(alignment) stream = StringIO() n = Align.write(alignment, stream, "stockholm") self.assertEqual(n, 1) stream.seek(0) alignments = Align.parse(stream, "stockholm") self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L'], ['V', 'E', 'R', 'Y', 'S', 'L', 'S', 'P', 'M', 'K', 'D', 'L', 'W', 'T', 'E', 'E', 'A', 'K', 'Y', 'R', 'R', 'W', 'L', 'E', 'V', 'E', 'L', 'A', 'V', 'T', 'R', 'A', 'Y', 'E', 'E', 'L', 'G', 'M', 'I', 'P', 'K', 'G', 'V', 'T', 'E', 'R', 'I', 'R', 'N', 'N', 'A', 'K', 'I', 'D', 'V', 'E', 'L', 'F', 'K', 'K', 'I', 'E', 'E', 'K', 'T', 'N', 'H', 'D', 'V', 'V', 'A', 'F', 'V', 'E', 'G', 'I', 'G', 'S', 'M', 'I', 'G', 'E', 'D', 'S', 'R', 'F', 'F', 'H', 'Y', 'G', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) stream.close() self.check_alignment_cath3(alignment) def test_io_nonstandard_annotations(self): """Test input and output of nonstandard GC, GS and GR annotation lines.""" # We write the alignment once to a stream and read it again to test # both inpiut and output. path = "Stockholm/example_nonstandardannotations.sth" alignments = Align.parse(path, "stockholm") alignment = next(alignments) self.assertNotIn("nonstandardgf", alignment.annotations.keys()) stream = StringIO() Align.write(alignment, stream, "stockholm") stream.seek(0) alignments = Align.parse(stream, "stockholm") alignment = next(alignments) stream.close() self.assertIn("nonstandardgc", alignment.column_annotations.keys()) self.assertIn("nonstandardgs", alignment.sequences[0].annotations.keys()) self.assertIn("nonstandardgr", alignment.sequences[0].letter_annotations.keys()) self.assertNotIn("nonstandardgf", alignment.annotations.keys()) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)