# Copyright 2005 by Michiel de Hoon. 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. """Test the NCBI XML parser.""" import os import unittest from Bio.Blast import NCBIXML E_VALUE_THRESH = 1e-10 class TestNCBIXML(unittest.TestCase): """Tests for the NCBI XML parser.""" def test_xml_2212L_blastp_001(self): """Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001).""" filename = "xml_2212L_blastp_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(len(alignments), 212) self.assertEqual(record.query_id, "gi|49176427|ref|NP_418280.3|") self.assertEqual(sum(len(a.hsps) for a in alignments), 212) alignment = alignments[0] self.assertEqual( alignment.title[:50], "gi|49176427|ref|NP_418280.3| component of Sec-inde" ) self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.20576e-46) self.assertEqual( hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.match[:75], "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.sbjct[:75], "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) alignment = alignments[1] self.assertEqual( alignment.title[:50], "gi|15804428|ref|NP_290468.1| twin arginine translo" ) self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.72609e-45) self.assertEqual( hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.match[:75], "MRLCLIIIYHR TCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.sbjct[:75], "MRLCLIIIYHRXTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) alignment = alignments[2] self.assertEqual( alignment.title[:50], "gi|74314349|ref|YP_312768.1| hypothetical protein " ) self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.72609e-45) self.assertEqual( hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.match[:75], "MR CLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) self.assertEqual( hsp.sbjct[:75], "MRPCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA", ) alignment = alignments[3] self.assertEqual( alignment.title[:50], "gi|75256240|ref|ZP_00727918.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 6.0872e-37) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) alignment = alignments[4] self.assertEqual( alignment.title[:50], "gi|148236|gb|AAA67633.1| o261 [Escherichia coli]" ) self.assertEqual(alignment.length, 261) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 6.74582e-28) self.assertEqual( hsp.query[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA", ) self.assertEqual( hsp.match[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA", ) self.assertEqual( hsp.sbjct[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA", ) alignment = alignments[5] self.assertEqual( alignment.title[:50], "gi|29143650|ref|NP_806992.1| sec-independent prote" ) self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.37251e-27) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLI+AVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDD+ KQDKTSQDADFTAK+IADKQ +", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIVAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDDAKQDKTSQDADFTAKSIADKQG-----E", ) alignment = alignments[6] self.assertEqual( alignment.title[:50], "gi|49609685|emb|CAG73118.1| sec-independent protei" ) self.assertEqual(alignment.length, 86) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.10205e-17) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEP--KQDKTSQDADFTAKTIADKQADTNQ", ) self.assertEqual( hsp.match[:75], "MGGIS+W LLIIAVIV+LLFGT KL ++GSDLGASIKGFKKAM DD+P DK DADF+ K+IAD Q+D ", ) self.assertEqual( hsp.sbjct[:75], "MGGISLWNLLIIAVIVILLFGTNKLRTLGSDLGASIKGFKKAMGDDQPSTNADKAQPDADFSTKSIADNQSD---", ) alignment = alignments[7] self.assertEqual( alignment.title[:50], "gi|37528238|ref|NP_931583.1| Sec-independent prote" ) self.assertEqual(alignment.length, 86) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.25087e-15) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDD-EPKQ-DKTSQDADFTAKTIADKQADTNQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKA+ DD +P+Q KTS DADF K I +KQ+ ", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAIGDDNQPQQAQKTSSDADFETKNITEKQS----", ) alignment = alignments[8] self.assertEqual( alignment.title[:50], "gi|59710656|ref|YP_203432.1| Sec-independent prote" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 5.01441e-15) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVI+VLLFGTKKL +GSDLG+++KGFKKA+S+DEP ++ +DADF + + K+A+T ++Q", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIIVLLFGTKKLRGVGSDLGSAVKGFKKAISEDEPAKE-AKKDADFVPQNLEKKEAETVEKQ", ) alignment = alignments[9] self.assertEqual( alignment.title[:50], "gi|54307340|ref|YP_128360.1| putative TatA protein" ) self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 7.2408e-14) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE--PKQDKTSQDADFTAKTIADKQADTNQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIA+I+VLLFGTKKL S+G DLG+++KGFKKA+ D+E K+D T DADF KT++ ++ + ", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIALIIVLLFGTKKLRSLGGDLGSAVKGFKKAIGDEELTVKKDNTEADADFEQKTLSKEEQQSED", ) alignment = alignments[10] self.assertEqual( alignment.title[:50], "gi|45437890|gb|AAS63439.1| Sec-independent protein" ) self.assertEqual(alignment.length, 88) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 1.61308e-13) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE----PKQDKTSQDADFTAKTIADKQADT", ) self.assertEqual( hsp.match[:75], "MG I QLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKAM DD DKTS DADF AK+I +KQ ", ) self.assertEqual( hsp.sbjct[:75], "MGSIGWAQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAMGDDSQTPPTNVDKTSNDADF-AKSITEKQ---", ) alignment = alignments[11] self.assertEqual( alignment.title[:50], "gi|75856473|ref|ZP_00764101.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.10675e-13) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG ++KGFKKAMS+DEP K +DADF K++ ++Q +++", ) self.assertEqual( hsp.sbjct[:75], "MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGGAVKGFKKAMSEDEPA--KNDKDADFEPKSLEEQQ----KKE", ) alignment = alignments[12] self.assertEqual( alignment.title[:50], "gi|75829371|ref|ZP_00758676.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.7515e-13) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQ", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQ", ) alignment = alignments[13] self.assertEqual( alignment.title[:50], "gi|75820019|ref|ZP_00750077.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.59357e-13) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQ", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQ", ) alignment = alignments[14] self.assertEqual( alignment.title[:50], "gi|28896872|ref|NP_796477.1| TatA protein [Vibrio " ) self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.32928e-12) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG+++KGFKKAMSD++ K +DADF K++ +Q Q++", ) self.assertEqual( hsp.sbjct[:75], "MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGSAVKGFKKAMSDED--SAKNEKDADFEPKSLEKQQ----QKE", ) alignment = alignments[15] self.assertEqual( alignment.title[:50], "gi|27364353|ref|NP_759881.1| Sec-independent prote" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +Q", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQSKQ", ) alignment = alignments[16] self.assertEqual( alignment.title[:50], "gi|37678364|ref|NP_932973.1| Sec-independent prote" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +Q", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQNKQ", ) alignment = alignments[17] self.assertEqual( alignment.title[:50], "gi|71277787|ref|YP_266931.1| Sec-independent prote" ) self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGI IWQL+I+AVIVVLLFGTKKL +IG DLG++IKGFK A+ +D K+ K S A+ T+ T+AD T +E ", ) self.assertEqual( hsp.sbjct[:75], "MGGIGIWQLVIVAVIVVLLFGTKKLRNIGGDLGSAIKGFKSAIGED--KEQKNS--AEKTSDTLADSSKSTTEEV", ) alignment = alignments[18] self.assertEqual( alignment.title[:50], "gi|68541995|ref|ZP_00581733.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.57533e-11) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTN", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLI+A+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIVALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESN", ) alignment = alignments[19] self.assertEqual( alignment.title[:50], "gi|77813363|ref|ZP_00812641.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.57533e-11) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTN", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLIIA+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESN", ) alignment = alignments[20] self.assertEqual( alignment.title[:50], "gi|52306607|gb|AAU37107.1| TatA protein [Mannheimi" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.36348e-11) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM++DEPK DA+F + D+ A E+", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMNEDEPK------DAEFKSLN-KDESATAGSEK", ) alignment = alignments[21] self.assertEqual( alignment.title[:50], "gi|75429751|ref|ZP_00732413.1| sec-independent pro" ) self.assertEqual(alignment.length, 74) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.36348e-11) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLII IVVLLFGTKKL ++GSDLG S+KGFKKAM+ +EPK DA+F + A+ A T +E+", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIVAIVVLLFGTKKLRTLGSDLGESVKGFKKAMA-EEPK------DAEFKSLDKAENTAQTKKEE", ) alignment = alignments[22] self.assertEqual( alignment.title[:50], "gi|32033565|ref|ZP_00133892.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 7.49305e-11) self.assertEqual( hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ", ) self.assertEqual( hsp.match[:75], "MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM+DD+ SQ D + + + K+A + +++", ) self.assertEqual( hsp.sbjct[:75], "MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMADDK------SQPQDASFEKVEAKEAASTEQK", ) alignment = alignments[23] self.assertEqual( alignment.title[:50], "gi|12722097|gb|AAK03773.1| unknown [Pasteurella mu" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[24] self.assertEqual( alignment.title[:50], "gi|68546478|ref|ZP_00586025.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[25] self.assertEqual( alignment.title[:50], "gi|33151888|ref|NP_873241.1| sec-independent prote" ) self.assertEqual(alignment.length, 74) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[26] self.assertEqual( alignment.title[:50], "gi|24375687|ref|NP_719730.1| Sec-independent prote" ) self.assertEqual(alignment.length, 88) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[27] self.assertEqual( alignment.title[:50], "gi|71278553|ref|YP_269744.1| Sec-independent prote" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[28] self.assertEqual( alignment.title[:50], "gi|69159855|gb|EAN71956.1| Twin-arginine transloca" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[29] self.assertEqual( alignment.title[:50], "gi|69949858|ref|ZP_00637822.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[30] self.assertEqual( alignment.title[:50], "gi|48863844|ref|ZP_00317737.1| hypothetical protei" ) self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[31] self.assertEqual( alignment.title[:50], "gi|77361831|ref|YP_341406.1| twin-arginine translo" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[32] self.assertEqual( alignment.title[:50], "gi|67676224|ref|ZP_00472975.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[33] self.assertEqual( alignment.title[:50], "gi|74317722|ref|YP_315462.1| twin-arginine translo" ) self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[34] self.assertEqual( alignment.title[:50], "gi|77166504|ref|YP_345029.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[35] self.assertEqual( alignment.title[:50], "gi|16128610|ref|NP_415160.1| component of Sec-inde" ) self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[36] self.assertEqual( alignment.title[:50], "gi|12831974|emb|CAC29147.1| TatA protein [Pseudomo" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[37] self.assertEqual( alignment.title[:50], "gi|32029972|ref|ZP_00132908.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[38] self.assertEqual(alignment.title[:50], "gi|455172|gb|AAA24073.1| ORF; putative") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[39] self.assertEqual(alignment.title[:50], "gi|1224007|gb|AAA92108.1| ORF4") self.assertEqual(alignment.length, 192) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[40] self.assertEqual( alignment.title[:50], "gi|68056990|gb|AAX87243.1| Sec-independent protein" ) self.assertEqual(alignment.length, 95) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[41] self.assertEqual( alignment.title[:50], "gi|56461470|ref|YP_156751.1| Sec-independent prote" ) self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[42] self.assertEqual( alignment.title[:50], "gi|76793313|ref|ZP_00775802.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[43] self.assertEqual( alignment.title[:50], "gi|42630489|ref|ZP_00156028.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[44] self.assertEqual( alignment.title[:50], "gi|1074302|pir||B64145 hypothetical protein HI0187" ) self.assertEqual(alignment.length, 109) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[45] self.assertEqual( alignment.title[:50], "gi|67641583|ref|ZP_00440359.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[46] self.assertEqual( alignment.title[:50], "gi|67545726|ref|ZP_00423646.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[47] self.assertEqual( alignment.title[:50], "gi|45435806|gb|AAS61363.1| sec-independent protein" ) self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[48] self.assertEqual( alignment.title[:50], "gi|49610761|emb|CAG74206.1| Sec-independent protei" ) self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[49] self.assertEqual( alignment.title[:50], "gi|67663266|ref|ZP_00460549.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[50] self.assertEqual( alignment.title[:50], "gi|33594634|ref|NP_882278.1| Sec-independent prote" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[51] self.assertEqual( alignment.title[:50], "gi|46310681|ref|ZP_00211309.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[52] self.assertEqual( alignment.title[:50], "gi|58584031|ref|YP_203047.1| sec-independent prote" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[53] self.assertEqual( alignment.title[:50], "gi|17429965|emb|CAD16649.1| PROBABLE SIGNAL PEPTID" ) self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[54] self.assertEqual( alignment.title[:50], "gi|47573371|ref|ZP_00243410.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[55] self.assertEqual( alignment.title[:50], "gi|16273687|ref|NP_438355.1| Sec-independent prote" ) self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[56] self.assertEqual( alignment.title[:50], "gi|73542784|ref|YP_297304.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[57] self.assertEqual( alignment.title[:50], "gi|26987777|ref|NP_743202.1| Sec-independent prote" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[58] self.assertEqual( alignment.title[:50], "gi|29142636|ref|NP_805978.1| sec-independent prote" ) self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[59] self.assertEqual( alignment.title[:50], "gi|18389921|gb|AAL68797.1| TatA [Ralstonia eutroph" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[60] self.assertEqual( alignment.title[:50], "gi|48781637|ref|ZP_00278228.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[61] self.assertEqual( alignment.title[:50], "gi|77456610|ref|YP_346115.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 92) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[62] self.assertEqual( alignment.title[:50], "gi|1684735|emb|CAA98158.1| ORF57 protein [Pseudomo" ) self.assertEqual(alignment.length, 57) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[63] self.assertEqual( alignment.title[:50], "gi|56476124|ref|YP_157713.1| Sec-independent prote" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[64] self.assertEqual( alignment.title[:50], "gi|34496078|ref|NP_900293.1| Sec-independent prote" ) self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[65] self.assertEqual( alignment.title[:50], "gi|67848115|ref|ZP_00503233.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[66] self.assertEqual( alignment.title[:50], "gi|26991692|ref|NP_747117.1| Sec-independent prote" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[67] self.assertEqual( alignment.title[:50], "gi|15601293|ref|NP_232924.1| tatA protein [Vibrio " ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[68] self.assertEqual( alignment.title[:50], "gi|66770480|ref|YP_245242.1| sec-independent prote" ) self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[69] self.assertEqual( alignment.title[:50], "gi|53804435|ref|YP_113945.1| Sec-independent prote" ) self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[70] self.assertEqual( alignment.title[:50], "gi|75825357|ref|ZP_00754793.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[71] self.assertEqual( alignment.title[:50], "gi|71908987|ref|YP_286574.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[72] self.assertEqual( alignment.title[:50], "gi|68526571|gb|EAN49542.1| Twin-arginine transloca" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[73] self.assertEqual( alignment.title[:50], "gi|71736448|ref|YP_272670.1| sec-independent prote" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[74] self.assertEqual( alignment.title[:50], "gi|56460344|ref|YP_155625.1| Sec-independent prote" ) self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[75] self.assertEqual( alignment.title[:50], "gi|68214708|ref|ZP_00566522.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[76] self.assertEqual( alignment.title[:50], "gi|30248650|ref|NP_840720.1| mttA/Hcf106 family [N" ) self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[77] self.assertEqual( alignment.title[:50], "gi|75822907|ref|ZP_00752458.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[78] self.assertEqual( alignment.title[:50], "gi|70733926|ref|YP_257566.1| sec-independent prote" ) self.assertEqual(alignment.length, 93) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[79] self.assertEqual( alignment.title[:50], "gi|63254358|gb|AAY35454.1| Twin-arginine transloca" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[80] self.assertEqual( alignment.title[:50], "gi|73354814|gb|AAZ75668.1| TatA [Pseudomonas syrin" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[81] self.assertEqual( alignment.title[:50], "gi|50083761|ref|YP_045271.1| Sec-independent prote" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[82] self.assertEqual( alignment.title[:50], "gi|71548504|ref|ZP_00668728.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[83] self.assertEqual( alignment.title[:50], "gi|55247002|gb|EAL42253.1| ENSANGP00000028218 [Ano" ) self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[84] self.assertEqual( alignment.title[:50], "gi|50084688|ref|YP_046198.1| Sec-independent prote" ) self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[85] self.assertEqual( alignment.title[:50], "gi|28872267|ref|NP_794886.1| sec-independent prote" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[86] self.assertEqual( alignment.title[:50], "gi|49082486|gb|AAT50643.1| PA5068 [synthetic const" ) self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[87] self.assertEqual( alignment.title[:50], "gi|53726598|ref|ZP_00141543.2| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[88] self.assertEqual( alignment.title[:50], "gi|68213616|ref|ZP_00565447.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 54) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[89] self.assertEqual( alignment.title[:50], "gi|74023810|ref|ZP_00694377.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[90] self.assertEqual( alignment.title[:50], "gi|71066554|ref|YP_265281.1| twin-arginine translo" ) self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[91] self.assertEqual( alignment.title[:50], "gi|15611372|ref|NP_223023.1| hypothetical protein " ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[92] self.assertEqual( alignment.title[:50], "gi|13471183|ref|NP_102752.1| sec-independent prote" ) self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[93] self.assertEqual( alignment.title[:50], "gi|42523995|ref|NP_969375.1| twin-arginine-depende" ) self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[94] self.assertEqual( alignment.title[:50], "gi|67158086|ref|ZP_00419176.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[95] self.assertEqual( alignment.title[:50], "gi|15644948|ref|NP_207118.1| conserved hypothetica" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[96] self.assertEqual( alignment.title[:50], "gi|13277311|emb|CAC34414.1| putative TatA protein " ) self.assertEqual(alignment.length, 61) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[97] self.assertEqual( alignment.title[:50], "gi|54298906|ref|YP_125275.1| Putative TatA protein" ) self.assertEqual(alignment.length, 61) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[98] self.assertEqual( alignment.title[:50], "gi|71363513|ref|ZP_00654157.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 94) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[99] self.assertEqual( alignment.title[:50], "gi|71362217|ref|ZP_00653377.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[100] self.assertEqual( alignment.title[:50], "gi|27379862|ref|NP_771391.1| hypothetical protein " ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[101] self.assertEqual( alignment.title[:50], "gi|39935914|ref|NP_948190.1| putative sec-independ" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[102] self.assertEqual( alignment.title[:50], "gi|17935600|ref|NP_532390.1| SEC-independent prote" ) self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[103] self.assertEqual( alignment.title[:50], "gi|62289827|ref|YP_221620.1| Sec-independent prote" ) self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[104] self.assertEqual( alignment.title[:50], "gi|23347697|gb|AAN29810.1| Sec-independent protein" ) self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[105] self.assertEqual( alignment.title[:50], "gi|75675971|ref|YP_318392.1| twin-arginine translo" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[106] self.assertEqual( alignment.title[:50], "gi|69928230|ref|ZP_00625391.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[107] self.assertEqual( alignment.title[:50], "gi|77689454|ref|ZP_00804635.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[108] self.assertEqual( alignment.title[:50], "gi|77743614|ref|ZP_00812071.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[109] self.assertEqual( alignment.title[:50], "gi|71066141|ref|YP_264868.1| twin-arginine translo" ) self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[110] self.assertEqual( alignment.title[:50], "gi|28199457|ref|NP_779771.1| SEC-independent prote" ) self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[111] self.assertEqual( alignment.title[:50], "gi|15837166|ref|NP_297854.1| hypothetical protein " ) self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[112] self.assertEqual( alignment.title[:50], "gi|15074462|emb|CAC46108.1| HYPOTHETICAL TRANSMEMB" ) self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[113] self.assertEqual( alignment.title[:50], "gi|27462871|gb|AAO15625.1| Sec-independent protein" ) self.assertEqual(alignment.length, 63) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[114] self.assertEqual( alignment.title[:50], "gi|35211273|dbj|BAC88652.1| gsl0711 [Gloeobacter v" ) self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[115] self.assertEqual( alignment.title[:50], "gi|34482347|emb|CAE09348.1| hypothetical protein [" ) self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[116] self.assertEqual( alignment.title[:50], "gi|32262257|gb|AAP77305.1| component of Sec-indepe" ) self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[117] self.assertEqual( alignment.title[:50], "gi|76261408|ref|ZP_00769019.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 62) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[118] self.assertEqual( alignment.title[:50], "gi|69933726|ref|ZP_00628928.1| sec-independent tra" ) self.assertEqual(alignment.length, 159) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[119] self.assertEqual( alignment.title[:50], "gi|15605662|ref|NP_213037.1| hypothetical protein " ) self.assertEqual(alignment.length, 59) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[120] self.assertEqual( alignment.title[:50], "gi|68538777|ref|ZP_00578553.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[121] self.assertEqual( alignment.title[:50], "gi|68136098|ref|ZP_00544086.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 130) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[122] self.assertEqual( alignment.title[:50], "gi|20259265|gb|AAM14368.1| putative Tha4 protein [" ) self.assertEqual(alignment.length, 147) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[123] self.assertEqual( alignment.title[:50], "gi|75910646|ref|YP_324942.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[124] self.assertEqual( alignment.title[:50], "gi|39982657|gb|AAR34117.1| twin-arginine transloca" ) self.assertEqual(alignment.length, 57) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[125] self.assertEqual( alignment.title[:50], "gi|33635687|emb|CAE22011.1| mttA/Hcf106 family [Pr" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[126] self.assertEqual( alignment.title[:50], "gi|76791934|ref|ZP_00774438.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[127] self.assertEqual( alignment.title[:50], "gi|23129516|ref|ZP_00111343.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[128] self.assertEqual( alignment.title[:50], "gi|48764199|ref|ZP_00268751.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 96) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[129] self.assertEqual( alignment.title[:50], "gi|15677995|ref|NP_273645.1| hypothetical protein " ) self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[130] self.assertEqual( alignment.title[:50], "gi|50917153|ref|XP_468973.1| putative sec-independ" ) self.assertEqual(alignment.length, 170) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[131] self.assertEqual( alignment.title[:50], "gi|16329622|ref|NP_440350.1| hypothetical protein " ) self.assertEqual(alignment.length, 126) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[132] self.assertEqual( alignment.title[:50], "gi|71083667|ref|YP_266387.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 66) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[133] self.assertEqual( alignment.title[:50], "gi|17130190|dbj|BAB72802.1| asl0845 [Nostoc sp. PC" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[134] self.assertEqual( alignment.title[:50], "gi|68246031|gb|EAN28138.1| Twin-arginine transloca" ) self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[135] self.assertEqual( alignment.title[:50], "gi|15604583|ref|NP_221101.1| hypothetical protein " ) self.assertEqual(alignment.length, 54) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[136] self.assertEqual( alignment.title[:50], "gi|77685166|ref|ZP_00800574.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[137] self.assertEqual( alignment.title[:50], "gi|39985226|gb|AAR36581.1| twin-arginine transloca" ) self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[138] self.assertEqual( alignment.title[:50], "gi|1825636|gb|AAB42258.1| Hypothetical protein ZK3" ) self.assertEqual(alignment.length, 312) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[139] self.assertEqual( alignment.title[:50], "gi|65321915|ref|ZP_00394874.1| COG5386: Cell surfa" ) self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[140] self.assertEqual( alignment.title[:50], "gi|30022625|ref|NP_834256.1| Cell surface protein " ) self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[141] self.assertEqual( alignment.title[:50], "gi|55623442|ref|XP_517520.1| PREDICTED: similar to" ) self.assertEqual(alignment.length, 234) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[142] self.assertEqual( alignment.title[:50], "gi|75762866|ref|ZP_00742681.1| Cell surface protei" ) self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[143] self.assertEqual( alignment.title[:50], "gi|22945598|gb|AAN10511.1| CG18497-PC, isoform C [" ) self.assertEqual(alignment.length, 5476) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[144] self.assertEqual( alignment.title[:50], "gi|10727420|gb|AAF51534.2| CG18497-PB, isoform B [" ) self.assertEqual(alignment.length, 5533) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[145] self.assertEqual( alignment.title[:50], "gi|10727421|gb|AAF51535.2| CG18497-PA, isoform A [" ) self.assertEqual(alignment.length, 5560) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[146] self.assertEqual( alignment.title[:50], "gi|71481981|ref|ZP_00661682.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[147] self.assertEqual( alignment.title[:50], "gi|71150623|ref|ZP_00649545.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[148] self.assertEqual( alignment.title[:50], "gi|20151563|gb|AAM11141.1| LD15253p [Drosophila me" ) self.assertEqual(alignment.length, 1521) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[149] self.assertEqual( alignment.title[:50], "gi|6979936|gb|AAF34661.1| split ends long isoform " ) self.assertEqual(alignment.length, 5554) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[150] self.assertEqual( alignment.title[:50], "gi|6467825|gb|AAF13218.1| Spen RNP motif protein l" ) self.assertEqual(alignment.length, 5533) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[151] self.assertEqual( alignment.title[:50], "gi|61102013|ref|ZP_00377467.1| hypothetical protei" ) self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[152] self.assertEqual( alignment.title[:50], "gi|68056232|ref|ZP_00540361.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[153] self.assertEqual( alignment.title[:50], "gi|68190120|gb|EAN04781.1| Twin-arginine transloca" ) self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[154] self.assertEqual( alignment.title[:50], "gi|15605663|ref|NP_213038.1| hypothetical protein " ) self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[155] self.assertEqual( alignment.title[:50], "gi|60493413|emb|CAH08199.1| aerotolerance-related " ) self.assertEqual(alignment.length, 238) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[156] self.assertEqual( alignment.title[:50], "gi|50877510|emb|CAG37350.1| related to Sec-indepen" ) self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[157] self.assertEqual( alignment.title[:50], "gi|42739647|gb|AAS43573.1| conserved domain protei" ) self.assertEqual(alignment.length, 236) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[158] self.assertEqual( alignment.title[:50], "gi|53713708|ref|YP_099700.1| conserved hypothetica" ) self.assertEqual(alignment.length, 238) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[159] self.assertEqual( alignment.title[:50], "gi|33860901|ref|NP_892462.1| mttA/Hcf106 family [P" ) self.assertEqual(alignment.length, 96) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[160] self.assertEqual( alignment.title[:50], "gi|48851224|ref|ZP_00305466.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[161] self.assertEqual( alignment.title[:50], "gi|67938449|ref|ZP_00530974.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[162] self.assertEqual( alignment.title[:50], "gi|45657833|ref|YP_001919.1| sec-independent prote" ) self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[163] self.assertEqual( alignment.title[:50], "gi|57238048|ref|YP_179297.1| twin-arginine translo" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[164] self.assertEqual( alignment.title[:50], "gi|56962648|ref|YP_174374.1| sec-independent prote" ) self.assertEqual(alignment.length, 63) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[165] self.assertEqual( alignment.title[:50], "gi|33239734|ref|NP_874676.1| Sec-independent prote" ) self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[166] self.assertEqual( alignment.title[:50], "gi|21674434|ref|NP_662499.1| Sec-independent prote" ) self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[167] self.assertEqual( alignment.title[:50], "gi|39968009|ref|XP_365395.1| hypothetical protein " ) self.assertEqual(alignment.length, 823) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[168] self.assertEqual( alignment.title[:50], "gi|4877986|gb|AAD31523.1| THA9 [Zea mays]" ) self.assertEqual(alignment.length, 169) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[169] self.assertEqual( alignment.title[:50], "gi|67934419|ref|ZP_00527476.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 56) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[170] self.assertEqual( alignment.title[:50], "gi|42523658|ref|NP_969038.1| twin-argine protein t" ) self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[171] self.assertEqual( alignment.title[:50], "gi|71546080|ref|ZP_00666945.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[172] self.assertEqual( alignment.title[:50], "gi|68002197|ref|ZP_00534828.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 60) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[173] self.assertEqual( alignment.title[:50], "gi|67481641|ref|XP_656170.1| hypothetical protein " ) self.assertEqual(alignment.length, 434) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[174] self.assertEqual( alignment.title[:50], "gi|50935447|ref|XP_477251.1| putative Calreticulin" ) self.assertEqual(alignment.length, 424) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[175] self.assertEqual( alignment.title[:50], "gi|50978634|ref|NP_001003013.1| acidic (leucine-ri" ) self.assertEqual(alignment.length, 249) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[176] self.assertEqual( alignment.title[:50], "gi|70936814|ref|XP_739300.1| 40S ribosomal subunit" ) self.assertEqual(alignment.length, 184) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[177] self.assertEqual( alignment.title[:50], "gi|68075857|ref|XP_679848.1| hypothetical protein " ) self.assertEqual(alignment.length, 340) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[178] self.assertEqual( alignment.title[:50], "gi|39594005|emb|CAE70115.1| Hypothetical protein C" ) self.assertEqual(alignment.length, 192) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[179] self.assertEqual( alignment.title[:50], "gi|66809957|ref|XP_638702.1| hypothetical protein " ) self.assertEqual(alignment.length, 721) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[180] self.assertEqual( alignment.title[:50], "gi|68550463|ref|ZP_00589911.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[181] self.assertEqual( alignment.title[:50], "gi|51473916|ref|YP_067673.1| TatA/E-like Sec-indep" ) self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[182] self.assertEqual( alignment.title[:50], "gi|61857708|ref|XP_612559.1| PREDICTED: similar to" ) self.assertEqual(alignment.length, 236) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[183] self.assertEqual( alignment.title[:50], "gi|39982651|gb|AAR34111.1| twin-arginine transloca" ) self.assertEqual(alignment.length, 59) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[184] self.assertEqual( alignment.title[:50], "gi|50877509|emb|CAG37349.1| related to Sec-indepen" ) self.assertEqual(alignment.length, 66) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[185] self.assertEqual( alignment.title[:50], "gi|52699323|ref|ZP_00340731.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[186] self.assertEqual( alignment.title[:50], "gi|62426215|ref|ZP_00381343.1| COG1826: Sec-indepe" ) self.assertEqual(alignment.length, 93) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[187] self.assertEqual( alignment.title[:50], "gi|11131838|sp|Q9SLY8|CRTC_ORYSA Calreticulin prec" ) self.assertEqual(alignment.length, 424) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[188] self.assertEqual( alignment.title[:50], "gi|56543690|gb|AAV89844.1| Sec-independent protein" ) self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[189] self.assertEqual( alignment.title[:50], "gi|67923730|ref|ZP_00517196.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 95) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[190] self.assertEqual( alignment.title[:50], "gi|67462585|ref|XP_647954.1| hypothetical protein " ) self.assertEqual(alignment.length, 140) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[191] self.assertEqual( alignment.title[:50], "gi|51970620|dbj|BAD44002.1| unknown protein [Arabi" ) self.assertEqual(alignment.length, 784) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[192] self.assertEqual( alignment.title[:50], "gi|34581241|ref|ZP_00142721.1| hypothetical protei" ) self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[193] self.assertEqual( alignment.title[:50], "gi|4877984|gb|AAD31522.1| THA4 [Zea mays]" ) self.assertEqual(alignment.length, 170) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[194] self.assertEqual( alignment.title[:50], "gi|9757886|dbj|BAB08393.1| unnamed protein product" ) self.assertEqual(alignment.length, 707) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[195] self.assertEqual( alignment.title[:50], "gi|32422107|ref|XP_331497.1| predicted protein [Ne" ) self.assertEqual(alignment.length, 216) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[196] self.assertEqual( alignment.title[:50], "gi|68552035|ref|ZP_00591428.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[197] self.assertEqual( alignment.title[:50], "gi|68177649|ref|ZP_00550794.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 58) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[198] self.assertEqual( alignment.title[:50], "gi|67934756|ref|ZP_00527782.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[199] self.assertEqual( alignment.title[:50], "gi|42550455|gb|EAA73298.1| hypothetical protein FG" ) self.assertEqual(alignment.length, 297) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[200] self.assertEqual( alignment.title[:50], "gi|15893083|ref|NP_360797.1| hypothetical protein " ) self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[201] self.assertEqual( alignment.title[:50], "gi|57233621|ref|YP_182297.1| twin-arginine translo" ) self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[202] self.assertEqual( alignment.title[:50], "gi|75908036|ref|YP_322332.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 56) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[203] self.assertEqual( alignment.title[:50], "gi|72383453|ref|YP_292808.1| Twin-arginine translo" ) self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[204] self.assertEqual( alignment.title[:50], "gi|1666185|emb|CAB04766.1| ORF13(1) [Rhodococcus e" ) self.assertEqual(alignment.length, 98) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[205] self.assertEqual( alignment.title[:50], "gi|72138252|ref|XP_800288.1| PREDICTED: hypothetic" ) self.assertEqual(alignment.length, 946) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[206] self.assertEqual( alignment.title[:50], "gi|67923190|ref|ZP_00516678.1| Twin-arginine trans" ) self.assertEqual(alignment.length, 50) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[207] self.assertEqual( alignment.title[:50], "gi|3329623|gb|AAC26930.1| Hypothetical protein F36" ) self.assertEqual(alignment.length, 335) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[208] self.assertEqual( alignment.title[:50], "gi|39597929|emb|CAE68621.1| Hypothetical protein C" ) self.assertEqual(alignment.length, 2691) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[209] self.assertEqual( alignment.title[:50], "gi|68182025|ref|ZP_00555006.1| hypothetical protei" ) self.assertEqual(alignment.length, 438) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[210] self.assertEqual( alignment.title[:50], "gi|21204492|dbj|BAB95189.1| ebh [Staphylococcus au" ) self.assertEqual(alignment.length, 9904) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) alignment = alignments[211] self.assertEqual( alignment.title[:50], "gi|39593039|emb|CAE64508.1| Hypothetical protein C" ) self.assertEqual(alignment.length, 960) self.assertEqual(len(alignment.hsps), 1) self.assertGreater(alignment.hsps[0].expect, E_VALUE_THRESH) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) def test_xml_2212L_blastn_001(self): """Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001).""" filename = "xml_2212L_blastn_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(record.query_id, "gi|1348916|gb|G26684.1|G26684") self.assertEqual(len(alignments), 2) self.assertEqual(sum(len(a.hsps) for a in alignments), 2) self.assertEqual( alignments[0].title[:50], "gi|9950606|gb|AE004854.1| Pseudomonas aeruginosa P", ) self.assertEqual(alignments[0].length, 11884) self.assertEqual(len(alignments[0].hsps), 1) self.assertGreater(alignments[0].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[1].title[:50], "gi|15073988|emb|AL591786.1|SME591786 Sinorhizobium", ) self.assertEqual(alignments[1].length, 299350) self.assertEqual(len(alignments[1].hsps), 1) self.assertGreater(alignments[1].hsps[0].expect, E_VALUE_THRESH) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) def test_xml_2212L_blastx_001(self): """Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001).""" filename = "xml_2212L_blastx_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(record.query_id, "gi|1347369|gb|G25137.1|G25137") self.assertEqual(len(alignments), 78) self.assertEqual(sum(len(a.hsps) for a in alignments), 84) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.score, 630.0) self.assertEqual(hsp.bits, 247.284) def test_xml_2212L_tblastn_001(self): """Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001).""" filename = "xml_2212L_tblastn_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(record.query_id, "gi|729325|sp|P39483|DHG2_BACME") self.assertEqual(len(alignments), 100) self.assertEqual(sum(len(a.hsps) for a in alignments), 127) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) def test_xml_2212L_tblastx_001(self): """Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001).""" filename = "xml_2212L_tblastx_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(record.query_id, "gi|1348853|gb|G26621.1|G26621") self.assertEqual(len(alignments), 10) self.assertEqual(sum(len(a.hsps) for a in alignments), 102) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) def test_xml_2218_blastp_001(self): """Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001).""" # NOTE - no date in version field, downloaded 2008/05/08 filename = "xml_2218_blastp_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) alignments = record.alignments self.assertEqual(record.query_id, "31493") self.assertEqual(len(alignments), 10) self.assertEqual(sum(len(a.hsps) for a in alignments), 14) self.assertEqual( alignments[0].title[:50], "gi|151942244|gb|EDN60600.1| cytosolic iron-sulfur ", ) self.assertEqual(alignments[0].length, 330) self.assertEqual(len(alignments[0].hsps), 1) self.assertGreater(alignments[0].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[1].title[:50], "gi|476059|emb|CAA55606.1| YBR0832 [Saccharomyces c", ) self.assertEqual(alignments[1].length, 535) self.assertEqual(len(alignments[1].hsps), 1) self.assertGreater(alignments[1].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[2].title[:50], "gi|6320473|ref|NP_010553.1| Essential protein invo", ) self.assertEqual(alignments[2].length, 330) self.assertEqual(len(alignments[2].hsps), 1) self.assertGreater(alignments[2].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[3].title[:50], "gi|61679798|pdb|1R5M|A Chain A, Crystal Structure ", ) self.assertEqual(alignments[3].length, 425) self.assertEqual(len(alignments[3].hsps), 1) self.assertGreater(alignments[3].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[4].title[:50], "gi|6319579|ref|NP_009661.1| WD40 repeat-containing", ) self.assertEqual(alignments[4].length, 535) self.assertEqual(len(alignments[4].hsps), 1) self.assertGreater(alignments[4].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[5].title[:50], "gi|151946495|gb|EDN64717.1| Sir4p-interacting fact", ) self.assertEqual(alignments[5].length, 535) self.assertEqual(len(alignments[5].hsps), 1) self.assertGreater(alignments[5].hsps[0].expect, E_VALUE_THRESH) self.assertEqual( alignments[6].title[:50], "gi|151943708|gb|EDN62018.1| nuclear pore complex s", ) self.assertEqual(alignments[6].length, 349) self.assertEqual(len(alignments[6].hsps), 2) self.assertGreater(alignments[6].hsps[0].expect, E_VALUE_THRESH) self.assertGreater(alignments[6].hsps[1].expect, E_VALUE_THRESH) self.assertEqual( alignments[7].title[:50], "gi|151567866|pdb|2PM7|B Chain B, Crystal Structure", ) self.assertEqual(alignments[7].length, 297) self.assertEqual(len(alignments[7].hsps), 2) self.assertGreater(alignments[7].hsps[0].expect, E_VALUE_THRESH) self.assertGreater(alignments[7].hsps[1].expect, E_VALUE_THRESH) self.assertEqual( alignments[8].title[:50], "gi|6321338|ref|NP_011415.1| Nuclear pore protein t", ) self.assertEqual(alignments[8].length, 349) self.assertEqual(len(alignments[8].hsps), 2) self.assertGreater(alignments[8].hsps[0].expect, E_VALUE_THRESH) self.assertGreater(alignments[8].hsps[1].expect, E_VALUE_THRESH) self.assertEqual( alignments[9].title[:50], "gi|151567870|pdb|2PM9|B Chain B, Crystal Structure", ) self.assertEqual(alignments[9].length, 297) self.assertEqual(len(alignments[9].hsps), 2) self.assertGreater(alignments[9].hsps[0].expect, E_VALUE_THRESH) self.assertGreater(alignments[9].hsps[1].expect, E_VALUE_THRESH) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) handle.close() def test_xml_2218_blastp_002(self): """Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002).""" filename = "xml_2218_blastp_002.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.query_id, "gi|585505|sp|Q08386|MOPB_RHOCA") self.assertEqual(len(record.alignments), 0) record = next(records) self.assertEqual(record.query_id, "gi|129628|sp|P07175.1|PARA_AGRTU") self.assertEqual(len(record.alignments), 0) self.assertRaises(StopIteration, next, records) def test_xml_2218L_blastp_001(self): """Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001).""" filename = "xml_2218L_blastp_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) self.assertEqual(record.query_id, "lcl|1_0") alignments = record.alignments self.assertEqual(len(alignments), 0) with open(datafile, "rb") as handle: record = NCBIXML.read(handle) def test_xml_2222_blastx_001(self): """Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001).""" # See also plain text file bt081.txt (matching output from blastx tool) filename = "xml_2222_blastx_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|4104054|gb|AH007193.1|SEG_CVIGS Centaurea vallesiaca 18S ribosomal RNA gene, partial sequence", ) self.assertEqual(record.query_letters, 1002) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 1) self.assertEqual(len(record.alignments), 1) self.assertEqual(len(record.alignments[0].hsps), 1) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|4218935|gb|AF074388.1|AF074388 Sambucus nigra hevein-like protein HLPf gene, partial cds", ) self.assertEqual(record.query_letters, 2050) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! # I used -num_descriptions 10 and -num_alignments 1 self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 2) self.assertEqual(len(record.alignments[1].hsps), 2) self.assertEqual(len(record.alignments[9].hsps), 2) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|5690369|gb|AF158246.1|AF158246 Cricetulus griseus glucose phosphate isomerase (GPI) gene, partial intron sequence", ) self.assertEqual(record.query_letters, 550) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 0) self.assertEqual(len(record.alignments), 0) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|5049839|gb|AI730987.1|AI730987 BNLGHi8354 Six-day Cotton fiber Gossypium hirsutum cDNA 5' similar to TUBULIN BETA-1 CHAIN gi|486734|pir|S35142 tubulin beta chain - white lupine gi|402636 (X70184) Beta tubulin 1 [Lupinus albus], mRNA sequence", ) self.assertEqual(record.query_letters, 655) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|5052071|gb|AF067555.1|AF067555 Phlox stansburyi internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence", ) self.assertEqual(record.query_letters, 623) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 2) self.assertEqual(len(record.alignments[9].hsps), 1) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|3176602|gb|U78617.1|LOU78617 Lathyrus odoratus phytochrome A (PHYA) gene, partial cds", ) self.assertEqual(record.query_letters, 309) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual( record.query, "gi|5817701|gb|AF142731.1|AF142731 Wisteria frutescens maturase-like protein (matK) gene, complete cds; chloroplast gene for chloroplast product", ) self.assertEqual(record.query_letters, 2551) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) self.assertRaises(StopIteration, next, records) def test_xml_2222_blastp_001(self): """Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001).""" # This is from blastp NOT blastall filename = "xml_2222_blastp_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, "2.2.22+") self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|3298468|dbj|BAA31520.1| SAMIPF") self.assertEqual(record.query_letters, 107) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) # self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) # NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) record = next(records) self.assertEqual( record.query, "gi|2781234|pdb|1JLY|B Chain B, Crystal Structure Of Amaranthus Caudatus Agglutinin", ) self.assertEqual(record.query_letters, 304) record = next(records) self.assertEqual( record.query, "gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING finger protein", ) self.assertEqual(record.query_letters, 600) record = next(records) self.assertEqual( record.query, "gi|671626|emb|CAA85685.1| rubisco large subunit" ) self.assertEqual(record.query_letters, 473) self.assertRaises(StopIteration, next, records) def test_xml_2218L_rpsblast_001(self): """Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001).""" # This is from old pgpblast command line tool, NOT new psiblast # NOTE - The parser currently returns three BLAST record objects. # The old text parser would return a single PSI BLAST record object with three rounds. # This may change... although it may require a PSI BLAST specific XML parser. filename = "xml_2218L_rpsblast_001.xml" datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, "2.2.18") self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 11) self.assertEqual(len(record.alignments), 11) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual( hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual(hsp.score, 680) self.assertEqual(hsp.expect, 4.72196e-70) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) self.assertEqual(len(record.alignments[1].hsps), 1) hsp = record.alignments[1].hsps[0] self.assertEqual(hsp.align_length, 77) self.assertEqual(hsp.identities, 36) self.assertEqual(hsp.positives, 49) self.assertEqual( hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQ", ) self.assertEqual( hsp.sbjct, "MAREEPYKGDYVGGVAKILQGYFANYYGFPNVSLRLAGEEANLSKTGHANAKAIVHEMIKVIKEASKPLR-RGKGFK", ) self.assertEqual( hsp.match, "MA+ EP KGDY GG KIL + G+P V+L+LAGEEAN + G K +H ++K+I +A KP R +G GF+", ) self.assertEqual(hsp.score, 181) self.assertEqual(hsp.expect, 3.03476e-12) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 77) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 76) record = next(records) self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, "2.2.18") self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 19) self.assertEqual(len(record.alignments), 19) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual( hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual(hsp.score, 590) self.assertEqual(hsp.expect, 1.28615e-59) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) record = next(records) self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, "2.2.18") self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 9) self.assertEqual(len(record.alignments), 9) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual( hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual( hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS", ) self.assertEqual(hsp.score, 535) self.assertEqual(hsp.expect, 3.43623e-53) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) # TODO - Can we detect the convergence status: # CONVERGED self.assertRaises(StopIteration, next, records) def test_xml_2900_blastp_001_v1(self): record = self._test_xml_2900_blastp_001("xml_2900_blastp_001.xml") description = record.descriptions[0] self.assertEqual(len(description.title), 4706) self.assertEqual( description.title[:300], "gi|447157535|ref|WP_001234791.1| MULTISPECIES: Sec-independent protein translocase subunit TatA [Shigella] >gi|24115132|ref|NP_709642.1| twin-arginine translocation protein TatA [Shigella flexneri 2a str. 301] >gi|82778983|ref|YP_405332.1| twin-arginine translocation protein TatA [Shigella dysenteri", ) description = record.descriptions[1] self.assertEqual(len(description.title), 106) self.assertEqual( description.title, "gi|91074959|gb|ABE09840.1| sec-independent twin-arginine translocase subunit tatA [Escherichia coli UTI89]", ) description = record.descriptions[2] self.assertEqual(len(description.title), 979) self.assertEqual( description.title[:300], "gi|73857826|gb|AAZ90533.1| conserved hypothetical protein [Shigella sonnei Ss046] >gi|331067587|gb|EGI38991.1| Sec-independent protein translocase protein TatA [Escherichia coli TA280] >gi|412965214|emb|CCK49144.1| sec-independent protein translocase protein tata/e homolog 2 [Escherichia coli chi712", ) description = record.descriptions[3] self.assertEqual(len(description.title), 260) self.assertEqual( description.title, "gi|25302684|pir||D86071 hypothetical protein tatA [imported] - Escherichia coli (strain O157:H7, substrain EDL933) >gi|12518713|gb|AAG59032.1|AE005614_12 twin arginine translocation protein; sec-independent protein export [Escherichia coli O157:H7 str. EDL933]", ) description = record.descriptions[4] self.assertEqual(len(description.title), 100) self.assertEqual( description.title, "gi|331072495|gb|EGI43827.1| Sec-independent protein translocase protein TatA [Escherichia coli H591]", ) description = record.descriptions[5] self.assertEqual(len(description.title), 120) self.assertEqual( description.title, "gi|808042844|pdb|2MN7|A Chain A, Solution structure of monomeric TatA of twin-arginine translocation system from E. coli", ) description = record.descriptions[6] self.assertEqual(len(description.title), 774516) self.assertEqual( description.title[:300], "gi|481023661|ref|WP_001295260.1| MULTISPECIES: Sec-independent protein translocase subunit TatA [Proteobacteria] >gi|15834020|ref|NP_312793.1| TatABCE protein translocation system subunit TatA [Escherichia coli O157:H7 str. Sakai] >gi|90111653|ref|NP_418280.4| twin arginine protein translocation sys", ) description = record.descriptions[7] self.assertEqual(len(description.title), 238) self.assertEqual( description.title, "gi|808042842|pdb|2MN6|B Chain B, Solution structure of dimeric TatA of twin-arginine translocation system from E. coli >gi|808042843|pdb|2MN6|A Chain A, Solution structure of dimeric TatA of twin-arginine translocation system from E. coli", ) description = record.descriptions[8] self.assertEqual(len(description.title), 2111) self.assertEqual( description.title[:300], "gi|491167042|ref|WP_005025412.1| MULTISPECIES: twin-arginine translocase subunit TatA [Enterobacteriaceae] >gi|320176770|gb|EFW51804.1| Twin-arginine translocation protein TatA [Shigella dysenteriae CDC 74-1112] >gi|391297993|gb|EIQ56018.1| twin arginine-targeting translocase, TatA/E family protein ", ) description = record.descriptions[9] self.assertEqual(len(description.title), 384) self.assertEqual( description.title[:300], "gi|332996954|gb|EGK16572.1| sec-independent translocase protein tatA [Shigella flexneri VA-6] >gi|391245379|gb|EIQ04650.1| twin arginine-targeting translocase, TatA/E family protein [Shigella flexneri K-1770] >gi|1411457050|emb|SRN34259.1| twin arginine translocase protein A [Shigella flexneri] >gi|", ) def test_xml_2900_blastp_001_v2(self): record = self._test_xml_2900_blastp_001("xml_2900_blastp_001_v2.xml") alignment = record.alignments[0] self.assertEqual( alignment.title, "gi|447157535|ref|WP_001234791.1| MULTISPECIES: Sec-independent protein translocase subunit TatA [Shigella]", ) description = record.descriptions[0] self.assertEqual( description.title, "gi|447157535|ref|WP_001234791.1| MULTISPECIES: Sec-independent protein translocase subunit TatA [Shigella]", ) self.assertEqual(len(description.items), 48) description_item = description.items[0] self.assertEqual(description_item.id, "gi|447157535|ref|WP_001234791.1|") self.assertEqual(description_item.accession, "WP_001234791") self.assertEqual( description_item.title, "MULTISPECIES: Sec-independent protein translocase subunit TatA [Shigella]", ) self.assertEqual(description_item.taxid, 620) self.assertEqual(description_item.sciname, "Shigella") def _test_xml_2900_blastp_001(self, filename): datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, "2.9.0+") self.assertEqual( record.query, "twin argininte translocase protein A [Escherichia coli K12]" ) self.assertEqual(record.query_letters, 103) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 194611632) self.assertEqual(record.database_sequences, 194611632) self.assertEqual(record.database_length, 2104817704) alignment = record.alignments[0] self.assertEqual(alignment.hit_id, "gi|447157535|ref|WP_001234791.1|") self.assertEqual(alignment.accession, "WP_001234791") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 103) self.assertEqual(hsp.identities, 103) self.assertEqual(hsp.positives, 103) self.assertEqual( hsp.query, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 532.0) self.assertEqual(hsp.expect, 1.71849e-68) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 103) alignment = record.alignments[1] self.assertEqual(alignment.hit_id, "gi|91074959|gb|ABE09840.1|") self.assertEqual(alignment.accession, "ABE09840") self.assertEqual( alignment.title, "gi|91074959|gb|ABE09840.1| sec-independent twin-arginine translocase subunit tatA [Escherichia coli UTI89]", ) self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 103) self.assertEqual(hsp.identities, 102) self.assertEqual(hsp.positives, 102) self.assertEqual( hsp.query, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKIEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAK EDAKRHDKEQV", ) self.assertEqual(hsp.score, 526.0) self.assertEqual(hsp.expect, 1.44614e-67) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 103) alignment = record.alignments[2] self.assertEqual(alignment.hit_id, "gi|73857826|gb|AAZ90533.1|") self.assertEqual(alignment.accession, "AAZ90533") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 103) self.assertEqual(hsp.identities, 102) self.assertEqual(hsp.positives, 102) self.assertEqual( hsp.query, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MRPCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MR CLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 525.0) self.assertEqual(hsp.expect, 1.80126e-67) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 103) alignment = record.alignments[3] self.assertEqual(alignment.hit_id, "gi|25302684|pir||D86071") self.assertEqual(alignment.accession, "D86071") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 103) self.assertEqual(hsp.identities, 102) self.assertEqual(hsp.positives, 102) self.assertEqual( hsp.query, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MRLCLIIIYHRXTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MRLCLIIIYHR TCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 525.0) self.assertEqual(hsp.expect, 2.10054e-67) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 103) alignment = record.alignments[4] self.assertEqual(alignment.hit_id, "gi|331072495|gb|EGI43827.1|") self.assertEqual(alignment.accession, "EGI43827") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 103) self.assertEqual(hsp.identities, 101) self.assertEqual(hsp.positives, 102) self.assertEqual( hsp.query, "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MRPCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQANTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MR CLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQA+TNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 522.0) self.assertEqual(hsp.expect, 5.11164e-67) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 103) alignment = record.alignments[5] self.assertEqual(alignment.hit_id, "gi|808042844|pdb|2MN7|A") self.assertEqual(alignment.accession, "2MN7_A") self.assertEqual(alignment.length, 97) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 89) self.assertEqual(hsp.identities, 89) self.assertEqual(hsp.positives, 89) self.assertEqual( hsp.query, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 449.0) self.assertEqual(hsp.expect, 5.99855e-56) self.assertEqual(hsp.query_start, 15) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 89) alignment = record.alignments[6] self.assertEqual(alignment.hit_id, "gi|481023661|ref|WP_001295260.1|") self.assertEqual(alignment.accession, "WP_001295260") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 89) self.assertEqual(hsp.identities, 89) self.assertEqual(hsp.positives, 89) self.assertEqual( hsp.query, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 448.0) self.assertEqual(hsp.expect, 8.86198e-56) self.assertEqual(hsp.query_start, 15) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 89) alignment = record.alignments[7] self.assertEqual(alignment.hit_id, "gi|808042842|pdb|2MN6|B") self.assertEqual(alignment.accession, "2MN6_B") self.assertEqual(alignment.length, 100) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 89) self.assertEqual(hsp.identities, 89) self.assertEqual(hsp.positives, 89) self.assertEqual( hsp.query, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 447.0) self.assertEqual(hsp.expect, 1.55019e-55) self.assertEqual(hsp.query_start, 15) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 4) self.assertEqual(hsp.sbjct_end, 92) alignment = record.alignments[8] self.assertEqual(alignment.hit_id, "gi|491167042|ref|WP_005025412.1|") self.assertEqual(alignment.accession, "WP_005025412") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 89) self.assertEqual(hsp.identities, 88) self.assertEqual(hsp.positives, 89) self.assertEqual( hsp.query, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDSDFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD+DFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 445.0) self.assertEqual(hsp.expect, 2.25306e-55) self.assertEqual(hsp.query_start, 15) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 89) alignment = record.alignments[9] self.assertEqual(alignment.hit_id, "gi|332996954|gb|EGK16572.1|") self.assertEqual(alignment.accession, "EGK16572") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 89) self.assertEqual(hsp.identities, 88) self.assertEqual(hsp.positives, 89) self.assertEqual( hsp.query, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.sbjct, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTISDKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual( hsp.match, "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTI+DKQADTNQEQAKTEDAKRHDKEQV", ) self.assertEqual(hsp.score, 445.0) self.assertEqual(hsp.expect, 2.25306e-55) self.assertEqual(hsp.query_start, 15) self.assertEqual(hsp.query_end, 103) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 89) self.assertEqual(len(record.descriptions), 10) description = record.descriptions[0] self.assertEqual(description.score, 532.0) self.assertEqual(description.e, 1.71849e-68) self.assertEqual(description.num_alignments, 1) description = record.descriptions[1] self.assertEqual(description.score, 526.0) self.assertEqual(description.e, 1.44614e-67) self.assertEqual(description.num_alignments, 1) description = record.descriptions[2] self.assertEqual(description.score, 525.0) self.assertEqual(description.e, 1.80126e-67) self.assertEqual(description.num_alignments, 1) description = record.descriptions[3] self.assertEqual(description.score, 525.0) self.assertEqual(description.e, 2.10054e-67) self.assertEqual(description.num_alignments, 1) description = record.descriptions[4] self.assertEqual(description.score, 522.0) self.assertEqual(description.e, 5.11164e-67) self.assertEqual(description.num_alignments, 1) description = record.descriptions[5] self.assertEqual(description.score, 449.0) self.assertEqual(description.e, 5.99855e-56) self.assertEqual(description.num_alignments, 1) description = record.descriptions[6] self.assertEqual(description.score, 448.0) self.assertEqual(description.e, 8.86198e-56) self.assertEqual(description.num_alignments, 1) description = record.descriptions[7] self.assertEqual(description.score, 447.0) self.assertEqual(description.e, 1.55019e-55) self.assertEqual(description.num_alignments, 1) description = record.descriptions[8] self.assertEqual(description.score, 445.0) self.assertEqual(description.e, 2.25306e-55) self.assertEqual(description.num_alignments, 1) description = record.descriptions[9] self.assertEqual(description.score, 445.0) self.assertEqual(description.e, 2.25306e-55) self.assertEqual(description.num_alignments, 1) return record def test_xml_2900_blastn_001_v1(self): self._test_xml_2900_blastn_001("xml_2900_blastn_001.xml") def test_xml_2900_blastn_001_v2(self): self._test_xml_2900_blastn_001("xml_2900_blastn_001_v2.xml") def _test_xml_2900_blastn_001(self, filename): datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) self.assertEqual(record.application, "BLASTN") self.assertEqual(record.version, "2.9.0+") self.assertEqual(record.query, "human STS STS_D11570, sequence tagged site") self.assertEqual(record.query_letters, 285) self.assertEqual( record.database, "GPIPE/10090/current/all_top_level GPIPE/10090/current/rna" ) self.assertEqual(record.num_sequences_in_database, 107382) self.assertEqual(record.database_sequences, 107382) self.assertEqual(record.database_length, 3164670549) alignment = record.alignments[0] self.assertEqual(alignment.hit_id, "gi|372099107|ref|NC_000069.6|") self.assertEqual(alignment.accession, "NC_000069") self.assertEqual(alignment.length, 160039680) self.assertEqual( alignment.title, "gi|372099107|ref|NC_000069.6| Mus musculus strain C57BL/6J chromosome 3, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 34) self.assertEqual(hsp.identities, 30) self.assertEqual(hsp.positives, 30) self.assertEqual(hsp.query, "GAATCCTAGAGGCTTGATTGGCCCAGG-CTGCTG") self.assertEqual(hsp.sbjct, "GAATCCTAGAGGCTGGACTGGCCCTGGCCTGCTG") self.assertEqual(hsp.match, "|||||||||||||| || |||||| || ||||||") self.assertEqual(hsp.score, 44.0) self.assertEqual(hsp.expect, 0.375311) self.assertEqual(hsp.query_start, 134) self.assertEqual(hsp.query_end, 166) self.assertEqual(hsp.sbjct_start, 101449177) self.assertEqual(hsp.sbjct_end, 101449144) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) alignment = record.alignments[1] self.assertEqual(alignment.hit_id, "gi|372099103|ref|NC_000073.6|") self.assertEqual(alignment.accession, "NC_000073") self.assertEqual(alignment.length, 145441459) self.assertEqual( alignment.title, "gi|372099103|ref|NC_000073.6| Mus musculus strain C57BL/6J chromosome 7, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 29) self.assertEqual(hsp.identities, 26) self.assertEqual(hsp.positives, 26) self.assertEqual(hsp.query, "GAAAGGAAATNAAAATGGAAAGTTCTTGT") self.assertEqual(hsp.sbjct, "GAAAGGAAAAAAAAATGGAAAGTTCTGGT") self.assertEqual(hsp.match, "||||||||| ||||||||||||||| ||") self.assertEqual(hsp.score, 44.0) self.assertEqual(hsp.expect, 0.375311) self.assertEqual(hsp.query_start, 205) self.assertEqual(hsp.query_end, 233) self.assertEqual(hsp.sbjct_start, 131772185) self.assertEqual(hsp.sbjct_end, 131772157) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) alignment = record.alignments[2] self.assertEqual(alignment.hit_id, "gi|372099106|ref|NC_000070.6|") self.assertEqual(alignment.accession, "NC_000070") self.assertEqual(alignment.length, 156508116) self.assertEqual( alignment.title, "gi|372099106|ref|NC_000070.6| Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 2) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 24) self.assertEqual(hsp.identities, 23) self.assertEqual(hsp.positives, 23) self.assertEqual(hsp.query, "CCAACACAGGCCAGCGACTTCTGG") self.assertEqual(hsp.sbjct, "CCAACACAGGCCAGCGGCTTCTGG") self.assertEqual(hsp.match, "|||||||||||||||| |||||||") self.assertEqual(hsp.score, 43.0) self.assertEqual(hsp.expect, 1.30996) self.assertEqual(hsp.query_start, 62) self.assertEqual(hsp.query_end, 85) self.assertEqual(hsp.sbjct_start, 9607562) self.assertEqual(hsp.sbjct_end, 9607539) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) hsp = alignment.hsps[1] self.assertEqual(hsp.align_length, 32) self.assertEqual(hsp.identities, 28) self.assertEqual(hsp.positives, 28) self.assertEqual(hsp.query, "GCCTGACATGG-GTAGCTGCTCAATAAATGCT") self.assertEqual(hsp.sbjct, "GCCTGGCATGAAGTAACTGCTCAATAAATGCT") self.assertEqual(hsp.match, "||||| |||| ||| ||||||||||||||||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 242) self.assertEqual(hsp.query_end, 272) self.assertEqual(hsp.sbjct_start, 142902532) self.assertEqual(hsp.sbjct_end, 142902563) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) alignment = record.alignments[3] self.assertEqual(alignment.hit_id, "gi|372099108|ref|NC_000068.7|") self.assertEqual(alignment.accession, "NC_000068") self.assertEqual(alignment.length, 182113224) self.assertEqual( alignment.title, "gi|372099108|ref|NC_000068.7| Mus musculus strain C57BL/6J chromosome 2, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 2) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 31) self.assertEqual(hsp.identities, 27) self.assertEqual(hsp.positives, 27) self.assertEqual(hsp.query, "AAGGCCTGACATGGGTAGCTGCTCAATAAAT") self.assertEqual(hsp.sbjct, "AAGTCCTGGCATGAGTAGTTGCTCAATAAAT") self.assertEqual(hsp.match, "||| |||| |||| |||| ||||||||||||") self.assertEqual(hsp.score, 42.0) self.assertEqual(hsp.expect, 1.30996) self.assertEqual(hsp.query_start, 239) self.assertEqual(hsp.query_end, 269) self.assertEqual(hsp.sbjct_start, 3799647) self.assertEqual(hsp.sbjct_end, 3799677) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) hsp = alignment.hsps[1] self.assertEqual(hsp.align_length, 25) self.assertEqual(hsp.identities, 23) self.assertEqual(hsp.positives, 23) self.assertEqual(hsp.query, "AAATNAAAATGGAAAGTTCTTGTAG") self.assertEqual(hsp.sbjct, "AAATGAAAATGGAAAGTTCTTATAG") self.assertEqual(hsp.match, "|||| |||||||||||||||| |||") self.assertEqual(hsp.score, 41.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 211) self.assertEqual(hsp.query_end, 235) self.assertEqual(hsp.sbjct_start, 70278960) self.assertEqual(hsp.sbjct_end, 70278984) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) alignment = record.alignments[4] self.assertEqual(alignment.hit_id, "gi|372099097|ref|NC_000079.6|") self.assertEqual(alignment.accession, "NC_000079") self.assertEqual(alignment.length, 120421639) self.assertEqual( alignment.title, "gi|372099097|ref|NC_000079.6| Mus musculus strain C57BL/6J chromosome 13, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 2) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 28) self.assertEqual(hsp.identities, 25) self.assertEqual(hsp.positives, 25) self.assertEqual(hsp.query, "AAGGAAATNAAAATGGAAAGTTCTTGTA") self.assertEqual(hsp.sbjct, "AAGGACATCAAAATGGAAAGTTCTTCTA") self.assertEqual(hsp.match, "||||| || |||||||||||||||| ||") self.assertEqual(hsp.score, 42.0) self.assertEqual(hsp.expect, 1.30996) self.assertEqual(hsp.query_start, 207) self.assertEqual(hsp.query_end, 234) self.assertEqual(hsp.sbjct_start, 26806584) self.assertEqual(hsp.sbjct_end, 26806557) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) hsp = alignment.hsps[1] self.assertEqual(hsp.align_length, 40) self.assertEqual(hsp.identities, 32) self.assertEqual(hsp.positives, 32) self.assertEqual(hsp.query, "AGCGCAAGGCCTGACATGGGTAGCTGCTCAATAAATGCTA") self.assertEqual(hsp.sbjct, "AGCGCAAGGCCTGACATAGGAAAATGTTCAGTGAATACTA") self.assertEqual(hsp.match, "||||||||||||||||| || | || ||| | ||| |||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 234) self.assertEqual(hsp.query_end, 273) self.assertEqual(hsp.sbjct_start, 56840340) self.assertEqual(hsp.sbjct_end, 56840301) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) alignment = record.alignments[5] self.assertEqual(alignment.hit_id, "gi|372099098|ref|NC_000078.6|") self.assertEqual(alignment.accession, "NC_000078") self.assertEqual(alignment.length, 120129022) self.assertEqual( alignment.title, "gi|372099098|ref|NC_000078.6| Mus musculus strain C57BL/6J chromosome 12, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 2) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 23) self.assertEqual(hsp.identities, 22) self.assertEqual(hsp.positives, 22) self.assertEqual(hsp.query, "CATCCATTCACACCCAACACAGG") self.assertEqual(hsp.sbjct, "CATCCATTCACACCCAGCACAGG") self.assertEqual(hsp.match, "|||||||||||||||| ||||||") self.assertEqual(hsp.score, 41.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 49) self.assertEqual(hsp.query_end, 71) self.assertEqual(hsp.sbjct_start, 113030663) self.assertEqual(hsp.sbjct_end, 113030685) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) hsp = alignment.hsps[1] self.assertEqual(hsp.align_length, 32) self.assertEqual(hsp.identities, 28) self.assertEqual(hsp.positives, 28) self.assertEqual(hsp.query, "TGTAGCGCAAGGCCTGACATGGGTAGCTGCTC") self.assertEqual(hsp.sbjct, "TGTAGCTCTAGGCCTGACATGGGT-GCTGGTC") self.assertEqual(hsp.match, "|||||| | ||||||||||||||| |||| ||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 231) self.assertEqual(hsp.query_end, 262) self.assertEqual(hsp.sbjct_start, 108990272) self.assertEqual(hsp.sbjct_end, 108990242) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) alignment = record.alignments[6] self.assertEqual(alignment.hit_id, "gi|372099109|ref|NC_000067.6|") self.assertEqual(alignment.accession, "NC_000067") self.assertEqual(alignment.length, 195471971) self.assertEqual( alignment.title, "gi|372099109|ref|NC_000067.6| Mus musculus strain C57BL/6J chromosome 1, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 43) self.assertEqual(hsp.identities, 35) self.assertEqual(hsp.positives, 35) self.assertEqual(hsp.query, "GCTCAGCCACAGACATGGTTTGTNACTNTTGAGCTTCTGTTCC") self.assertEqual(hsp.sbjct, "GCTCAGCCACATACATGGTTT-TAAGTGTTGAGGCTCT-TTCC") self.assertEqual(hsp.match, "||||||||||| ||||||||| | | | ||||| ||| ||||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 87) self.assertEqual(hsp.query_end, 129) self.assertEqual(hsp.sbjct_start, 65190108) self.assertEqual(hsp.sbjct_end, 65190148) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) alignment = record.alignments[7] self.assertEqual(alignment.hit_id, "gi|372099101|ref|NC_000075.6|") self.assertEqual(alignment.accession, "NC_000075") self.assertEqual(alignment.length, 124595110) self.assertEqual( alignment.title, "gi|372099101|ref|NC_000075.6| Mus musculus strain C57BL/6J chromosome 9, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 47) self.assertEqual(hsp.identities, 36) self.assertEqual(hsp.positives, 36) self.assertEqual(hsp.query, "CAAGGCCTGACATGGGTAGCTGCTCAATAAATGCTAGTNTGTTATTT") self.assertEqual(hsp.sbjct, "CAAAGCCTGACAGGTATGACTGCTCAATAAATACTATTTTTTTTTTT") self.assertEqual(hsp.match, "||| |||||||| | | ||||||||||||| ||| | | || |||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 238) self.assertEqual(hsp.query_end, 284) self.assertEqual(hsp.sbjct_start, 58227241) self.assertEqual(hsp.sbjct_end, 58227195) self.assertEqual(hsp.frame, (1, -1)) self.assertEqual(hsp.strand, ("Plus", "Minus")) alignment = record.alignments[8] self.assertEqual(alignment.hit_id, "gi|372099100|ref|NC_000076.6|") self.assertEqual(alignment.accession, "NC_000076") self.assertEqual(alignment.length, 130694993) self.assertEqual( alignment.title, "gi|372099100|ref|NC_000076.6| Mus musculus strain C57BL/6J chromosome 10, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 20) self.assertEqual(hsp.identities, 20) self.assertEqual(hsp.positives, 20) self.assertEqual(hsp.query, "AGCTGCTCAATAAATGCTAG") self.assertEqual(hsp.sbjct, "AGCTGCTCAATAAATGCTAG") self.assertEqual(hsp.match, "||||||||||||||||||||") self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 255) self.assertEqual(hsp.query_end, 274) self.assertEqual(hsp.sbjct_start, 119337186) self.assertEqual(hsp.sbjct_end, 119337205) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) alignment = record.alignments[9] self.assertEqual(alignment.hit_id, "gi|372099094|ref|NC_000082.6|") self.assertEqual(alignment.accession, "NC_000082") self.assertEqual(alignment.length, 98207768) self.assertEqual( alignment.title, "gi|372099094|ref|NC_000082.6| Mus musculus strain C57BL/6J chromosome 16, GRCm38.p4 C57BL/6J", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 56) self.assertEqual(hsp.identities, 43) self.assertEqual(hsp.positives, 43) self.assertEqual( hsp.query, "GGAGGCAAAGAATCCCTACCTCCT-AGGGGTGA-AAGGAAATNAAAATGGAAAGTT" ) self.assertEqual( hsp.sbjct, "GGAGGCAAAGAATCCCTACATTGTGACAGCTGATAAAGAAGGTAAAATGGAAAATT" ) self.assertEqual( hsp.match, "||||||||||||||||||| | | | | ||| || ||| |||||||||| ||" ) self.assertEqual(hsp.score, 40.0) self.assertEqual(hsp.expect, 4.57222) self.assertEqual(hsp.query_start, 175) self.assertEqual(hsp.query_end, 228) self.assertEqual(hsp.sbjct_start, 18854780) self.assertEqual(hsp.sbjct_end, 18854835) self.assertEqual(hsp.frame, (1, 1)) self.assertEqual(hsp.strand, ("Plus", "Plus")) self.assertEqual(len(record.descriptions), 10) description = record.descriptions[0] self.assertEqual(description.score, 44.0) self.assertEqual(description.e, 0.375311) self.assertEqual(description.num_alignments, 1) description = record.descriptions[1] self.assertEqual(description.score, 44.0) self.assertEqual(description.e, 0.375311) self.assertEqual(description.num_alignments, 1) description = record.descriptions[2] self.assertEqual(description.score, 43.0) self.assertEqual(description.e, 1.30996) self.assertEqual(description.num_alignments, 2) description = record.descriptions[3] self.assertEqual(description.score, 42.0) self.assertEqual(description.e, 1.30996) self.assertEqual(description.num_alignments, 2) description = record.descriptions[4] self.assertEqual(description.score, 42.0) self.assertEqual(description.e, 1.30996) self.assertEqual(description.num_alignments, 2) description = record.descriptions[5] self.assertEqual(description.score, 41.0) self.assertEqual(description.e, 4.57222) self.assertEqual(description.num_alignments, 2) description = record.descriptions[6] self.assertEqual(description.score, 40.0) self.assertEqual(description.e, 4.57222) self.assertEqual(description.num_alignments, 1) description = record.descriptions[7] self.assertEqual(description.score, 40.0) self.assertEqual(description.e, 4.57222) self.assertEqual(description.num_alignments, 1) description = record.descriptions[8] self.assertEqual(description.score, 40.0) self.assertEqual(description.e, 4.57222) self.assertEqual(description.num_alignments, 1) description = record.descriptions[9] self.assertEqual(description.score, 40.0) self.assertEqual(description.e, 4.57222) self.assertEqual(description.num_alignments, 1) def test_xml_2900_blastx_001_v1(self): self._test_xml_2900_blastx_001("xml_2900_blastx_001.xml") def test_xml_2900_blastx_001_v2(self): self._test_xml_2900_blastx_001("xml_2900_blastx_001_v2.xml") def _test_xml_2900_blastx_001(self, filename): datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, "2.9.0+") self.assertEqual( record.query, "MAAD0534.RAR Schistosoma mansoni, adult worm (J.C.Parra) Schistosoma mansoni cDNA clone MAAD0534.RAR 5' end similar to S. mansoni actin mRNA, complete cds, mRNA sequence", ) self.assertEqual(record.query_letters, 365) self.assertEqual(record.database, "nr") alignment = record.alignments[0] self.assertEqual(alignment.hit_id, "gi|1530504495|emb|VDM03167.1|") self.assertEqual(alignment.accession, "VDM03167") self.assertEqual(alignment.length, 132) self.assertEqual( alignment.title, "gi|1530504495|emb|VDM03167.1| unnamed protein product, partial [Schistocephalus solidus]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 81) self.assertEqual(hsp.positives, 83) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADEEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "MADEEVQALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 408.0) self.assertEqual(hsp.bits, 161.77) self.assertEqual(hsp.expect, 8.11609e-49) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[1] self.assertEqual(alignment.hit_id, "gi|510859078|gb|EPB74633.1|") self.assertEqual(alignment.accession, "EPB74633") self.assertEqual(alignment.length, 119) self.assertEqual( alignment.title, "gi|510859078|gb|EPB74633.1| hypothetical protein ANCCEY_06263 [Ancylostoma ceylanicum]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 115) self.assertEqual(hsp.identities, 81) self.assertEqual(hsp.positives, 85) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTELHCIRKP", ) self.assertEqual( hsp.sbjct, "MCDDDVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAHSILKP", ) self.assertEqual( hsp.match, "M D++V ALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE H I KP", ) self.assertEqual(hsp.score, 405.0) self.assertEqual(hsp.expect, 1.40046e-48) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 364) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 115) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[2] self.assertEqual(alignment.hit_id, "gi|684409690|ref|XP_009175831.1|") self.assertEqual(alignment.accession, "XP_009175831") self.assertEqual(alignment.length, 246) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 81) self.assertEqual(hsp.positives, 83) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADEEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "MADEEVQALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 413.0) self.assertEqual(hsp.expect, 4.40404e-48) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[3] self.assertEqual(alignment.hit_id, "gi|449710331|gb|EMD49430.1|") self.assertEqual(alignment.accession, "EMD49430") self.assertEqual(alignment.length, 124) self.assertEqual( alignment.title, "gi|449710331|gb|EMD49430.1| actin, putative, partial [Entamoeba histolytica KU27]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 78) self.assertEqual(hsp.positives, 81) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MGDEEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHVSVMAGMGQKDAYVGDEAQSKRGILTLKYPIEHGIVNNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "M DEEVQALVVDNGSGMCKAG ++ P G KD+YVGDEAQSKRGILTLKYPIEHGIV NWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 401.0) self.assertEqual(hsp.expect, 9.0486e-48) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[4] self.assertEqual(alignment.hit_id, "gi|257215766|emb|CAX83035.1|") self.assertEqual(alignment.accession, "CAX83035") self.assertEqual(alignment.length, 252) self.assertEqual( alignment.title, "gi|257215766|emb|CAX83035.1| Actin-2, partial [Schistosoma japonicum]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 81) self.assertEqual(hsp.positives, 83) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADEEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "MADEEVQALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 411.0) self.assertEqual(hsp.expect, 1.00219e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[5] self.assertEqual(alignment.hit_id, "gi|1535393712|emb|VDP83060.1|") self.assertEqual(alignment.accession, "VDP83060") self.assertEqual(alignment.length, 209) self.assertEqual( alignment.title, "gi|1535393712|emb|VDP83060.1| unnamed protein product, partial [Echinostoma caproni]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 80) self.assertEqual(hsp.positives, 83) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADDEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "MAD+EVQALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 407.0) self.assertEqual(hsp.expect, 1.16397e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[6] self.assertEqual(alignment.hit_id, "gi|312773|emb|CAA50205.1|") self.assertEqual(alignment.accession, "CAA50205") self.assertEqual(alignment.length, 137) self.assertEqual( alignment.title, "gi|312773|emb|CAA50205.1| actin, partial [Entamoeba histolytica]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 78) self.assertEqual(hsp.positives, 81) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MGDEEVQALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHVSVMAGMGQKDAYVGDEAQSKRGILTLKYPIEHGIVNNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "M DEEVQALVVDNGSGMCKAG ++ P G KD+YVGDEAQSKRGILTLKYPIEHGIV NWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 401.0) self.assertEqual(hsp.expect, 1.25869e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[7] self.assertEqual(alignment.hit_id, "gi|1530341495|emb|VDN44756.1|") self.assertEqual(alignment.accession, "VDN44756") self.assertEqual(alignment.length, 145) self.assertEqual( alignment.title, "gi|1530341495|emb|VDN44756.1| unnamed protein product, partial [Dibothriocephalus latus]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 78) self.assertEqual(hsp.positives, 82) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MGDEDVQALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "M DE+VQALV+DNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 400.0) self.assertEqual(hsp.expect, 1.78336e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[8] self.assertEqual(alignment.hit_id, "gi|1524877828|ref|XP_027046469.1|") self.assertEqual(alignment.accession, "XP_027046469") self.assertEqual(alignment.length, 122) self.assertEqual( alignment.title, "gi|1524877828|ref|XP_027046469.1| actin-1, partial [Pocillopora damicornis]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 78) self.assertEqual(hsp.positives, 82) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRIAPEEHPILLTE", ) self.assertEqual( hsp.match, "MADEEV ALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELR+APEEHP+LLTE", ) self.assertEqual(hsp.score, 398.0) self.assertEqual(hsp.expect, 1.93331e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) alignment = record.alignments[9] self.assertEqual(alignment.hit_id, "gi|1524877860|ref|XP_027046487.1|") self.assertEqual(alignment.accession, "XP_027046487") self.assertEqual(alignment.length, 134) self.assertEqual( alignment.title, "gi|1524877860|ref|XP_027046487.1| actin-1-like [Pocillopora damicornis]", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 108) self.assertEqual(hsp.identities, 79) self.assertEqual(hsp.positives, 82) self.assertEqual( hsp.query, "MADEEVQALVVDNGSGMCKAGIRW**CTKSSIPFHRWTTSTSRCDGWYGSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.sbjct, "MADEDVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual( hsp.match, "MADE+V ALVVDNGSGMCKAG ++ P G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE", ) self.assertEqual(hsp.score, 399.0) self.assertEqual(hsp.expect, 2.36088e-47) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 108) self.assertEqual(hsp.frame, (2, 0)) self.assertEqual(len(record.descriptions), 10) description = record.descriptions[0] self.assertEqual( description.title, "gi|1530504495|emb|VDM03167.1| unnamed protein product, partial [Schistocephalus solidus]", ) self.assertEqual(description.score, 408.0) self.assertEqual(description.e, 8.11609e-49) self.assertEqual(description.num_alignments, 1) description = record.descriptions[1] self.assertEqual( description.title, "gi|510859078|gb|EPB74633.1| hypothetical protein ANCCEY_06263 [Ancylostoma ceylanicum]", ) self.assertEqual(description.score, 405.0) self.assertEqual(description.e, 1.40046e-48) self.assertEqual(description.num_alignments, 1) description = record.descriptions[2] self.assertEqual(description.score, 413.0) self.assertEqual(description.e, 4.40404e-48) self.assertEqual(description.num_alignments, 1) description = record.descriptions[3] self.assertEqual( description.title, "gi|449710331|gb|EMD49430.1| actin, putative, partial [Entamoeba histolytica KU27]", ) self.assertEqual(description.score, 401.0) self.assertEqual(description.e, 9.0486e-48) self.assertEqual(description.num_alignments, 1) description = record.descriptions[4] self.assertEqual( description.title, "gi|257215766|emb|CAX83035.1| Actin-2, partial [Schistosoma japonicum]", ) self.assertEqual(description.score, 411.0) self.assertEqual(description.e, 1.00219e-47) self.assertEqual(description.num_alignments, 1) description = record.descriptions[5] self.assertEqual( description.title, "gi|1535393712|emb|VDP83060.1| unnamed protein product, partial [Echinostoma caproni]", ) self.assertEqual(description.score, 407.0) self.assertEqual(description.e, 1.16397e-47) self.assertEqual(description.num_alignments, 1) description = record.descriptions[6] self.assertEqual( description.title, "gi|312773|emb|CAA50205.1| actin, partial [Entamoeba histolytica]", ) self.assertEqual(description.score, 401.0) self.assertEqual(description.e, 1.25869e-47) self.assertEqual(description.num_alignments, 1) description = record.descriptions[7] self.assertEqual( description.title, "gi|1530341495|emb|VDN44756.1| unnamed protein product, partial [Dibothriocephalus latus]", ) self.assertEqual(description.score, 400.0) self.assertEqual(description.e, 1.78336e-47) self.assertEqual(description.num_alignments, 1) description = record.descriptions[8] self.assertEqual( description.title, "gi|1524877828|ref|XP_027046469.1| actin-1, partial [Pocillopora damicornis]", ) self.assertEqual(description.score, 398.0) self.assertEqual(description.e, 1.93331e-47) self.assertEqual(description.num_alignments, 1) description = record.descriptions[9] self.assertEqual( description.title, "gi|1524877860|ref|XP_027046487.1| actin-1-like [Pocillopora damicornis]", ) self.assertEqual(description.score, 399.0) self.assertEqual(description.e, 2.36088e-47) self.assertEqual(description.num_alignments, 1) def test_xml_2900_tblastn_001_v1(self): self._test_xml_2900_tblastn_001("xml_2900_tblastn_001.xml") def test_xml_2900_tblastn_001_v2(self): self._test_xml_2900_tblastn_001("xml_2900_tblastn_001_v2.xml") def _test_xml_2900_tblastn_001(self, filename): datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertRaises(StopIteration, next, records) self.assertEqual(record.application, "TBLASTN") self.assertEqual(record.version, "2.9.0+") self.assertEqual(record.query, "tim [Helicobacter acinonychis str. Sheeba]") self.assertEqual(record.query_letters, 234) self.assertEqual(record.database, "nr") alignment = record.alignments[4] self.assertEqual(alignment.hit_id, "gi|1143706535|gb|CP018823.1|") self.assertEqual(alignment.accession, "CP018823") self.assertEqual(alignment.length, 1618480) self.assertEqual( alignment.title, "gi|1143706535|gb|CP018823.1| Helicobacter pylori strain PMSS1 complete genome", ) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 234) self.assertEqual(hsp.identities, 218) self.assertEqual(hsp.positives, 223) self.assertEqual( hsp.query, "MTKIAMANFKSAMPIFKSHAYLKELEKTLKPQHCDRVFVFPDFLGLLPNAFLHFTLGVQNAYPKDCGAFTGEITSKHLEELKINTLLIGHSERRVLLKESPNFLKEKFDFFKDKKFKIVYCIGEDLKTREKGLGAVKEFLNEQLENIDLDYQNLIVAYEPIWAIGTGKSASLEDIYLTHGFLKQHLNQKMPLLYGGSVNTQNAKEILGIDSVDGLLIGSTSLELENFKTIISFL", ) self.assertEqual( hsp.sbjct, "MTKIAMANFKSAMPIFKSHAYLKELEKTLKPQHFDRVFVFPDFLGLLPNSFLHFTLGVQNAYPRDCGAFTGEITSKHLEELKIHTLLIGHSERRVLLKESPSFLKEKFDFFKDKNFKIVYCIGEDLTTREKGFKAVKEFLNEQLENIDLNYSNLIVAYEPIWAIGTKKSASLEDIYLTHGFLKQILNQKTPLLYGGSVNTQNAKEILGIDSVDGLLIGSASWELENFKTIISFL", ) self.assertEqual( hsp.match, "MTKIAMANFKSAMPIFKSHAYLKELEKTLKPQH DRVFVFPDFLGLLPN+FLHFTLGVQNAYP+DCGAFTGEITSKHLEELKI+TLLIGHSERRVLLKESP+FLKEKFDFFKDK FKIVYCIGEDL TREKG AVKEFLNEQLENIDL+Y NLIVAYEPIWAIGT KSASLEDIYLTHGFLKQ LNQK PLLYGGSVNTQNAKEILGIDSVDGLLIGS S ELENFKTIISFL", ) self.assertEqual(hsp.score, 1136.0) self.assertEqual(hsp.bits, 442.195) self.assertEqual(hsp.expect, 2.08707e-139) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 234) self.assertEqual(hsp.sbjct_start, 190464) self.assertEqual(hsp.sbjct_end, 191165) self.assertEqual(hsp.frame, (0, 3)) self.assertEqual(len(record.descriptions), 10) description = record.descriptions[4] self.assertEqual( description.title, "gi|1143706535|gb|CP018823.1| Helicobacter pylori strain PMSS1 complete genome", ) self.assertEqual(description.score, 1136.0) self.assertEqual(description.e, 2.08707e-139) self.assertEqual(description.num_alignments, 1) def test_xml_2900_tblastx_001_v1(self): self._test_xml_2900_tblastx_001("xml_2900_tblastx_001.xml") def test_xml_2900_tblastx_001_v2(self): self._test_xml_2900_tblastx_001("xml_2900_tblastx_001_v2.xml") def _test_xml_2900_tblastx_001(self, filename): datafile = os.path.join("Blast", filename) with open(datafile, "rb") as handle: records = NCBIXML.parse(handle) record = next(records) self.assertEqual(record.application, "TBLASTX") self.assertEqual(record.version, "2.9.0+") self.assertEqual( record.query, "MAAD0534.RAR Schistosoma mansoni, adult worm (J.C.Parra) Schistosoma mansoni cDNA clone MAAD0534.RAR 5' end similar to S. mansoni actin mRNA, complete cds, mRNA sequence", ) self.assertEqual(record.query_letters, 365) self.assertEqual(record.database, "nr") alignment = record.alignments[4] self.assertEqual(alignment.hit_id, "gi|1590279025|ref|XM_028307351.1|") self.assertEqual(alignment.accession, "XM_028307351") self.assertEqual(alignment.length, 1599) self.assertEqual( alignment.title, "gi|1590279025|ref|XM_028307351.1| PREDICTED: Ostrinia furnacalis actin, cytoplasmic A3a (LOC114354791), mRNA", ) self.assertEqual(len(alignment.hsps), 12) hsp = alignment.hsps[0] self.assertEqual(hsp.align_length, 60) self.assertEqual(hsp.identities, 59) self.assertEqual(hsp.positives, 59) self.assertEqual( hsp.query, "GSKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE" ) self.assertEqual( hsp.sbjct, "GQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE" ) self.assertEqual( hsp.match, "G KDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE" ) self.assertEqual(hsp.score, 325.0) self.assertEqual(hsp.expect, 7.83523e-61) self.assertEqual(hsp.query_start, 164) self.assertEqual(hsp.query_end, 343) self.assertEqual(hsp.sbjct_start, 389) self.assertEqual(hsp.sbjct_end, 568) self.assertEqual(hsp.frame, (2, 2)) hsp = alignment.hsps[1] self.assertEqual(hsp.align_length, 36) self.assertEqual(hsp.identities, 33) self.assertEqual(hsp.positives, 33) self.assertEqual(hsp.query, "GCAKLGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQK") self.assertEqual(hsp.sbjct, "GMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQK") self.assertEqual(hsp.match, "G K GFAGDDAPRAVFPSIVGRPRHQGVMVGMGQK") self.assertEqual(hsp.score, 174.0) self.assertEqual(hsp.expect, 7.83523e-61) self.assertEqual(hsp.query_start, 66) self.assertEqual(hsp.query_end, 173) self.assertEqual(hsp.sbjct_start, 290) self.assertEqual(hsp.sbjct_end, 397) self.assertEqual(hsp.frame, (3, 2)) hsp = alignment.hsps[2] self.assertEqual(hsp.align_length, 21) self.assertEqual(hsp.identities, 19) self.assertEqual(hsp.positives, 19) self.assertEqual(hsp.query, "MADEEVQALVVDNGSGMCKAG") self.assertEqual(hsp.sbjct, "MCDEEVAALVVDNGSGMCKAG") self.assertEqual(hsp.match, "M DEEV ALVVDNGSGMCKAG") self.assertEqual(hsp.score, 97.0) self.assertEqual(hsp.expect, 7.83523e-61) self.assertEqual(hsp.query_start, 20) self.assertEqual(hsp.query_end, 82) self.assertEqual(hsp.sbjct_start, 245) self.assertEqual(hsp.sbjct_end, 307) self.assertEqual(hsp.frame, (2, 2)) hsp = alignment.hsps[3] self.assertEqual(hsp.align_length, 61) self.assertEqual(hsp.identities, 48) self.assertEqual(hsp.positives, 52) self.assertEqual( hsp.query, "SSVNRTGCSSGATRNSL*NV*CQIFSMSSQFVTIPCSIGYFSVRIPRFDCASSPT*LSFDP" ) self.assertEqual( hsp.sbjct, "ASVRRTGCSSGATRSSL*KV*CQIFSMSSQFVTIPCSMGYLSVRMPLLLWASSPT*ESFCP" ) self.assertEqual( hsp.match, "+SV RTGCSSGATR+SL* V*CQIFSMSSQFVTIPCS+GY SVR+P ASSPT* SF P" ) self.assertEqual(hsp.score, 225.0) self.assertEqual(hsp.expect, 3.26469e-39) self.assertEqual(hsp.query_start, 163) self.assertEqual(hsp.query_end, 345) self.assertEqual(hsp.sbjct_start, 388) self.assertEqual(hsp.sbjct_end, 570) self.assertEqual(hsp.frame, (-3, -1)) hsp = alignment.hsps[4] self.assertEqual(hsp.align_length, 36) self.assertEqual(hsp.identities, 24) self.assertEqual(hsp.positives, 28) self.assertEqual(hsp.query, "F*PIPTITP*CRGRPTMEGNTALGASSPANPSFAHP") self.assertEqual(hsp.sbjct, "FCPMPTITPWWRGRPTIDGNTARGASSPAKPALHIP") self.assertEqual(hsp.match, "F P+PTITP RGRPT++GNTA GASSPA P+ P") self.assertEqual(hsp.score, 121.0) self.assertEqual(hsp.expect, 3.26469e-39) self.assertEqual(hsp.query_start, 65) self.assertEqual(hsp.query_end, 172) self.assertEqual(hsp.sbjct_start, 289) self.assertEqual(hsp.sbjct_end, 396) self.assertEqual(hsp.frame, (-2, -1)) hsp = alignment.hsps[5] self.assertEqual(hsp.align_length, 26) self.assertEqual(hsp.identities, 18) self.assertEqual(hsp.positives, 22) self.assertEqual(hsp.query, "PALHIPDPLSTTRA*TSSSAMIIFQL") self.assertEqual(hsp.sbjct, "PALHIPDPLSTTNAATSSSHILVYLL") self.assertEqual(hsp.match, "PALHIPDPLSTT A TSSS ++++ L") self.assertEqual(hsp.score, 91.0) self.assertEqual(hsp.expect, 3.26469e-39) self.assertEqual(hsp.query_start, 4) self.assertEqual(hsp.query_end, 81) self.assertEqual(hsp.sbjct_start, 229) self.assertEqual(hsp.sbjct_end, 306) self.assertEqual(hsp.frame, (-3, -1)) hsp = alignment.hsps[6] self.assertEqual(hsp.align_length, 57) self.assertEqual(hsp.identities, 34) self.assertEqual(hsp.positives, 43) self.assertEqual( hsp.query, "GQQDRVFFWSHTQFIVECVMPDLLHVIPVRHNTVFDWVFQCENTTFRLCFITDVAVF" ) self.assertEqual( hsp.sbjct, "GKKDWVFLGSDTEFIVEGVMPDLLHVIPVCDDSVFDGVFECEDASLALGLISDVGVF" ) self.assertEqual( hsp.match, "G++D VF S T+FIVE VMPDLLHVIPV ++VFD VF+CE+ + L I+DV VF" ) self.assertEqual(hsp.score, 167.0) self.assertEqual(hsp.expect, 2.27039e-16) self.assertEqual(hsp.query_start, 170) self.assertEqual(hsp.query_end, 340) self.assertEqual(hsp.sbjct_start, 395) self.assertEqual(hsp.sbjct_end, 565) self.assertEqual(hsp.frame, (-2, -3)) hsp = alignment.hsps[7] self.assertEqual(hsp.align_length, 32) self.assertEqual(hsp.identities, 13) self.assertEqual(hsp.positives, 23) self.assertEqual(hsp.query, "LTHTNHHTLMSRSSNDGREYCSWCIITSESQL") self.assertEqual(hsp.sbjct, "LSHANHHTLVARAAHDRWEHGAGRVIARETGL") self.assertEqual(hsp.match, "L+H NHHTL++R+++D E+ + +I E+ L") self.assertEqual(hsp.score, 69.0) self.assertEqual(hsp.expect, 2.27039e-16) self.assertEqual(hsp.query_start, 75) self.assertEqual(hsp.query_end, 170) self.assertEqual(hsp.sbjct_start, 299) self.assertEqual(hsp.sbjct_end, 394) self.assertEqual(hsp.frame, (-1, -3)) hsp = alignment.hsps[8] self.assertEqual(hsp.align_length, 64) self.assertEqual(hsp.identities, 36) self.assertEqual(hsp.positives, 44) self.assertEqual( hsp.query, "KRQLRR**STIETWYSHTEIPNRTRYCDELG*HGEDLASHILQ*IACGSRRTPCPVDRAPLYPK", ) self.assertEqual( hsp.sbjct, "KRLLRRR*GPEQERHPHTQIPHRTRNRHKLG*HGEDLASHLLQ*TPCRSRGTPSPSYRSPPEPQ", ) self.assertEqual( hsp.match, "KR LRR * + + HT+IP+RTR +LG*HGEDLASH+LQ* C SR TP P R+P P+", ) self.assertEqual(hsp.score, 160.0) self.assertEqual(hsp.expect, 2.96635e-13) self.assertEqual(hsp.query_start, 169) self.assertEqual(hsp.query_end, 360) self.assertEqual(hsp.sbjct_start, 394) self.assertEqual(hsp.sbjct_end, 585) self.assertEqual(hsp.frame, (1, 1)) hsp = alignment.hsps[9] self.assertEqual(hsp.align_length, 20) self.assertEqual(hsp.identities, 8) self.assertEqual(hsp.positives, 12) self.assertEqual(hsp.query, "IPFHRWTTSTSRCDGWYGSK") self.assertEqual(hsp.sbjct, "VPIDRGPPAPPGCDGWHGTK") self.assertEqual(hsp.match, "+P R + CDGW+G+K") self.assertEqual(hsp.score, 53.0) self.assertEqual(hsp.expect, 2.96635e-13) self.assertEqual(hsp.query_start, 113) self.assertEqual(hsp.query_end, 172) self.assertEqual(hsp.sbjct_start, 337) self.assertEqual(hsp.sbjct_end, 396) self.assertEqual(hsp.frame, (2, 1)) hsp = alignment.hsps[10] self.assertEqual(hsp.align_length, 48) self.assertEqual(hsp.identities, 29) self.assertEqual(hsp.positives, 33) self.assertEqual(hsp.query, "FGYNGARSTGQGVLLEPHAIHCRMCDARSSPCHPSSSQYRVRLGISV*") self.assertEqual(hsp.sbjct, "WGSGGLR*EGLGVPRERHGVHCRRCDARSSPCHPSL*RFRVRWGI*V*") self.assertEqual(hsp.match, "+G G R G GV E H +HCR CDARSSPCHPS ++RVR GI V*") self.assertEqual(hsp.score, 142.0) self.assertEqual(hsp.expect, 2.61074e-08) self.assertEqual(hsp.query_start, 216) self.assertEqual(hsp.query_end, 359) self.assertEqual(hsp.sbjct_start, 441) self.assertEqual(hsp.sbjct_end, 584) self.assertEqual(hsp.frame, (-1, -2)) hsp = alignment.hsps[11] self.assertEqual(hsp.align_length, 58) self.assertEqual(hsp.identities, 33) self.assertEqual(hsp.positives, 37) self.assertEqual( hsp.query, "QKTATSVMKHNRNVVFSH*NTQSNTVL*RTGMTWRRSGITHSTMNCVWLQKNTLSC*P" ) self.assertEqual( hsp.sbjct, "KKTPTSEMRPRAREASSHSNTPSNTESSQTGMTWRRSGITPSTMNSVSLPRNTQSFLP" ) self.assertEqual( hsp.match, "+KT TS M+ SH NT SNT +TGMTWRRSGIT STMN V L +NT S P" ) self.assertEqual(hsp.score, 141.0) self.assertEqual(hsp.expect, 3.58672e-08) self.assertEqual(hsp.query_start, 168) self.assertEqual(hsp.query_end, 341) self.assertEqual(hsp.sbjct_start, 393) self.assertEqual(hsp.sbjct_end, 566) self.assertEqual(hsp.frame, (3, 3)) self.assertEqual(len(record.descriptions), 10) description = record.descriptions[4] self.assertEqual( description.title, "gi|1590279025|ref|XM_028307351.1| PREDICTED: Ostrinia furnacalis actin, cytoplasmic A3a " "(LOC114354791), mRNA", ) self.assertEqual(description.score, 325.0) self.assertEqual(description.e, 7.83523e-61) self.assertEqual(description.num_alignments, 12) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)