# Copyright 2006-2014 by Peter Cock. All rights reserved. # Revisions copyright 2011 Brandon Invergo. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Bio.Align.phylip module.""" import unittest from io import StringIO from Bio import Align try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.phylip." ) from None class TestPhylipReading(unittest.TestCase): def check_reading_writing(self, path): alignments = Align.parse(path, "phylip") stream = StringIO() n = Align.write(alignments, stream, "phylip") self.assertEqual(n, 1) alignments = Align.parse(path, "phylip") alignment = next(alignments) stream.seek(0) saved_alignments = Align.parse(stream, "phylip") saved_alignment = next(saved_alignments) with self.assertRaises(StopIteration): next(saved_alignments) self.assertEqual(len(alignment), len(saved_alignment)) for i, (sequence, saved_sequence) in enumerate( zip(alignment.sequences, saved_alignment.sequences) ): self.assertEqual(sequence.id, saved_sequence.id) self.assertEqual(sequence.seq, saved_sequence.seq) self.assertEqual(alignment[i], saved_alignment[i]) self.assertTrue( np.array_equal(alignment.coordinates, saved_alignment.coordinates) ) def test_one(self): path = "Phylip/one.dat" with open(path) as stream: alignments = Align.parse(stream, "phylip") self.check_one(alignments) alignments = iter(alignments) self.check_one(alignments) with Align.parse(path, "phylip") as alignments: self.check_one(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "phylip") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def check_one(self, alignments): alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 8) self.assertEqual(alignment.sequences[0].id, "V_Harveyi_") self.assertEqual(alignment.sequences[1].id, "B_subtilis") self.assertEqual(alignment.sequences[2].id, "B_subtilis") self.assertEqual(alignment.sequences[3].id, "YA80_HAEIN") self.assertEqual(alignment.sequences[4].id, "FLIY_ECOLI") self.assertEqual(alignment.sequences[5].id, "E_coli_Gln") self.assertEqual(alignment.sequences[6].id, "Deinococcu") self.assertEqual(alignment.sequences[7].id, "HISJ_E_COL") self.assertEqual( alignment.sequences[0].seq, "MKNWIKVAVAAIALSAATVQAATEVKVGMSGRYFPFTFVKQDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDTGIEHDVALGRADAFIMDRLSALELIKKTGLPLQLAGEPFETIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK", ) self.assertEqual( alignment.sequences[1].seq, "MKMKKWTVLVVAALLAVLSACGNGNSSSKEDDNVLHVGATGQSYPFAYKENGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIAQIKKTGLPLKLAGDPIVYEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH", ) self.assertEqual( alignment.sequences[2].seq, "MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVGKTDREDKYDFSDKYTTSRAVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATNAGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLNYLKTSGNKNVKIAFETGEPQSTYFTFRKGSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK", ) self.assertEqual( alignment.sequences[3].seq, "MKKLLFTTALLTGAIAFSTFSHAGEIADRVEKTKTLLVGTEGTYAPFTFHDKSGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKAAGAQILVVDGLAQSLELIKQGRAEATINDKLAVLDYFKQHPNSGLKIAYDRGDKTPTAFAFLQGEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ", ) self.assertEqual( alignment.sequences[4].seq, "MKLAHLGRQALMGVMAVALVAGMSVKSFADEGLLNKVKERGTLLVGLEGTYPPFSFQGDDGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVTGEAFSRQESGVALRKGNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK", ) self.assertEqual( alignment.sequences[5].seq, "MKSVLKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK", ) self.assertEqual( alignment.sequences[6].seq, "MKKSLLSLKLSGLLVPSVLALSLSACSSPSSTLNQGTLKIAMEGTYPPFTSKNEQGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTGDIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNYIINDQKLPVRGAGQIGDAAPVGIALKKGNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP", ) self.assertEqual( alignment.sequences[7].seq, "MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG", ) self.assertEqual( alignment[0], "--MKNWIKVAVAAIA--LSAA------------------TVQAATEVKVGMSGRYFPFTFVKQ--DKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDG-AQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKT-GLPLQLAGEPFETI-----QNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK----", ) self.assertEqual( alignment[1], "MKMKKWTVLVVAALLAVLSACG------------NGNSSSKEDDNVLHVGATGQSYPFAYKEN--GKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAG-TQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKT-GLPLKLAGDPIVYE-----QVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH", ) self.assertEqual( alignment[2], "MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVG-KTDREDKYDFSDKYTTSR-AVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATN----AGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGEPQ-----STYFTFRKGS--GEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK----", ) self.assertEqual( alignment[3], "MKKLLFTTALLTGAIAFSTF-----------SHAGEIADRVEKTKTLLVGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSG-GVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKA----AGAQILVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGDKT-----PTAFAFLQGE--DALITKFNQVLEALRQDGTLKQISIEWFGYDITQ----", ) self.assertEqual( alignment[4], "MKLAHLGRQALMGVMAVALVAG---MSVKSFADEG-LLNKVKERGTLLVGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNV--QGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKT-NDTLAVTGEAFSRQ-----ESGVALRKGN--EDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK----", ) self.assertEqual( alignment[5], "--MKSVLKVSLAALTLAFAVS------------------SHAADKKLVVATDTAFVPFEFKQG--DKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSG-LLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLEAQ-----QYGIAFPKGS--DELRDKVNGALKTLRENGTYNEIYKKWFGTEPK-----", ) self.assertEqual( alignment[6], "-MKKSLLSLKLSGLLVPSVLALS--------LSACSSPSSTLNQGTLKIAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTG---DIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNY-IINDQ-KLPVRGAGQIGDAA-----PVGIALKKGN--SALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP---", ) self.assertEqual( alignment[7], "MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQP-TVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKED--NELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG---", ) self.assertEqual( str(alignment), """\ V_Harveyi 0 --MKNWIKVAVAAIA--LSAA------------------TVQAATEVKVGMSGRYFPFTF B_subtili 0 MKMKKWTVLVVAALLAVLSACG------------NGNSSSKEDDNVLHVGATGQSYPFAY B_subtili 0 MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTY YA80_HAEI 0 MKKLLFTTALLTGAIAFSTF-----------SHAGEIADRVEKTKTLLVGTEGTYAPFTF FLIY_ECOL 0 MKLAHLGRQALMGVMAVALVAG---MSVKSFADEG-LLNKVKERGTLLVGLEGTYPPFSF E_coli_Gl 0 --MKSVLKVSLAALTLAFAVS------------------SHAADKKLVVATDTAFVPFEF Deinococc 0 -MKKSLLSLKLSGLLVPSVLALS--------LSACSSPSSTLNQGTLKIAMEGTYPPFTS HISJ_E_CO 0 MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIGTDPTYAPFES V_Harveyi 38 VKQ--DKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARK B_subtili 48 KEN--GKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERK B_subtili 60 HDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVG-KTDRE YA80_HAEI 49 HDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERL FLIY_ECOL 56 QGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERK E_coli_Gl 40 KQG--DKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERK Deinococc 51 KNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQ HISJ_E_CO 41 KNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQ V_Harveyi 96 AKYLFADPYVVDG-AQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINI B_subtili 106 ETYNFTKPYAYAG-TQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINI B_subtili 119 DKYDFSDKYTTSR-AVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATN----AGAKV YA80_HAEI 108 KKYSFTTPYNYSG-GVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKA----AGAQI FLIY_ECOL 115 KKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNV--QGVDV E_coli_Gl 98 KAIDFSDGYYKSG-LLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDL Deinococc 110 NSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTG---DIKI HISJ_E_CO 100 QEIAFTDKLYAADSRLVVAKNSDIQP-TVESLKGKRVGVLQGTTQETFGNEHWAPKGIEI V_Harveyi 155 KTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKT-GLPLQLAGEPFETI-----QNAW B_subtili 165 KTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKT-GLPLKLAGDPIVYE-----QVAF B_subtili 174 EGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGEPQ-----STYF YA80_HAEI 163 LVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGDKT-----PTAF FLIY_ECOL 173 RTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKT-NDTLAVTGEAFSRQ-----ESGV E_coli_Gl 155 RQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLEAQ-----QYGI Deinococc 167 VTYPGAPEILADLVAGRIDAAYNDRLVVNY-IINDQ-KLPVRGAGQIGDAA-----PVGI HISJ_E_CO 159 VSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGM V_Harveyi 206 PFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK---- 248 B_subtili 218 PFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH 264 B_subtili 228 TFRKGS--GEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK---- 268 YA80_HAEI 217 AFLQGE--DALITKFNQVLEALRQDGTLKQISIEWFGYDITQ---- 257 FLIY_ECOL 226 ALRKGN--EDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK---- 266 E_coli_Gl 209 AFPKGS--DELRDKVNGALKTLRENGTYNEIYKKWFGTEPK----- 248 Deinococc 220 ALKKGN--SALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP--- 261 HISJ_E_CO 219 GLRKED--NELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG--- 260 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array( [[ 0, 0, 0, 13, 13, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 41, 41, 41, 90, 91, 109, 109, 121, 122, 146, 147, 148, 149, 150, 151, 160, 160, 183, 183, 188, 188, 202, 202, 212, 214, 247, 248, 248, 248], [ 0, 1, 2, 15, 17, 20, 21, 22, 22, 22, 22, 22, 23, 24, 27, 28, 51, 51, 51, 100, 101, 119, 119, 131, 132, 156, 157, 158, 159, 160, 161, 170, 172, 195, 195, 200, 200, 214, 214, 224, 226, 259, 260, 261, 264], [ 0, 1, 2, 15, 17, 20, 21, 22, 23, 25, 31, 34, 35, 36, 39, 40, 63, 64, 65, 114, 114, 132, 132, 144, 145, 169, 169, 169, 169, 169, 170, 179, 181, 204, 204, 209, 210, 224, 224, 234, 234, 267, 268, 268, 268], [ 0, 1, 2, 15, 17, 20, 20, 20, 20, 20, 20, 23, 24, 25, 28, 29, 52, 52, 53, 102, 103, 121, 121, 133, 134, 158, 158, 158, 158, 158, 159, 168, 170, 193, 193, 198, 199, 213, 213, 223, 223, 256, 257, 257, 257], [ 0, 1, 2, 15, 17, 20, 21, 22, 22, 22, 28, 31, 32, 32, 35, 36, 59, 59, 60, 109, 110, 128, 129, 141, 142, 166, 167, 168, 168, 168, 169, 178, 180, 203, 203, 208, 208, 222, 222, 232, 232, 265, 266, 266, 266], [ 0, 0, 0, 13, 15, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 43, 43, 43, 92, 93, 111, 111, 123, 124, 148, 149, 149, 149, 150, 151, 160, 162, 185, 185, 190, 191, 205, 205, 215, 215, 248, 248, 248, 248], [ 0, 0, 1, 14, 16, 19, 20, 21, 22, 22, 22, 25, 26, 27, 30, 31, 54, 54, 55, 104, 105, 123, 124, 136, 137, 161, 162, 163, 163, 163, 163, 172, 174, 197, 197, 202, 202, 216, 216, 226, 226, 259, 260, 261, 261], [ 0, 1, 2, 15, 17, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 44, 44, 45, 94, 95, 113, 114, 126, 126, 150, 151, 152, 153, 154, 155, 164, 166, 189, 190, 195, 196, 210, 215, 225, 225, 258, 259, 260, 260]]), # fmt: on ) ) self.assertEqual( format(alignment, "phylip"), """\ 8 286 V_Harveyi_--MKNWIKVAVAAIA--LSAA------------------TVQAATEVKVGMSGRYFPFTFVKQ--DKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDG-AQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKT-GLPLQLAGEPFETI-----QNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK---- B_subtilisMKMKKWTVLVVAALLAVLSACG------------NGNSSSKEDDNVLHVGATGQSYPFAYKEN--GKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAG-TQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKT-GLPLKLAGDPIVYE-----QVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH B_subtilisMKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVG-KTDREDKYDFSDKYTTSR-AVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATN----AGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGEPQ-----STYFTFRKGS--GEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK---- YA80_HAEINMKKLLFTTALLTGAIAFSTF-----------SHAGEIADRVEKTKTLLVGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSG-GVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKA----AGAQILVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGDKT-----PTAFAFLQGE--DALITKFNQVLEALRQDGTLKQISIEWFGYDITQ---- FLIY_ECOLIMKLAHLGRQALMGVMAVALVAG---MSVKSFADEG-LLNKVKERGTLLVGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNV--QGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKT-NDTLAVTGEAFSRQ-----ESGVALRKGN--EDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK---- E_coli_Gln--MKSVLKVSLAALTLAFAVS------------------SHAADKKLVVATDTAFVPFEFKQG--DKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSG-LLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLEAQ-----QYGIAFPKGS--DELRDKVNGALKTLRENGTYNEIYKKWFGTEPK----- Deinococcu-MKKSLLSLKLSGLLVPSVLALS--------LSACSSPSSTLNQGTLKIAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTG---DIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNY-IINDQ-KLPVRGAGQIGDAA-----PVGIALKKGN--SALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP--- HISJ_E_COLMKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQP-TVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKED--NELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG--- """, ) def test_two_and_three(self): paths = ("Phylip/two.dat", "Phylip/three.dat") # derived from http://atgc.lirmm.fr/phyml/usersguide.html for path in paths: with open(path) as stream: alignments = Align.parse(stream, "phylip") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 5) self.assertEqual(alignment.sequences[0].id, "Tax1") self.assertEqual(alignment.sequences[1].id, "Tax2") self.assertEqual(alignment.sequences[2].id, "Tax3") self.assertEqual(alignment.sequences[3].id, "Tax4") self.assertEqual(alignment.sequences[4].id, "Tax5") self.assertEqual( alignment.sequences[0].seq, "CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT", ) self.assertEqual( alignment.sequences[1].seq, "CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT", ) self.assertEqual( alignment.sequences[2].seq, "CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT", ) self.assertEqual( alignment.sequences[3].seq, "TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT", ) self.assertEqual( alignment.sequences[4].seq, "CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT", ) self.assertEqual( alignment[0], "CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT", ) self.assertEqual( alignment[1], "CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT", ) self.assertEqual( alignment[2], "CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT", ) self.assertEqual( alignment[3], "TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT", ) self.assertEqual( alignment[4], "CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT", ) self.check_reading_writing(path) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 60], [0, 60], [0, 60], [0, 60], [0, 60]]), ) ) self.assertEqual( str(alignment), """\ Tax1 0 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT Tax2 0 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT Tax3 0 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT Tax4 0 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT Tax5 0 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT Tax1 60 Tax2 60 Tax3 60 Tax4 60 Tax5 60 """, ) self.assertEqual( format(alignment, "phylip"), """\ 5 60 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT """, ) def test_four(self): path = "Phylip/four.dat" # File derived from here: # http://evolution.genetics.washington.edu/phylip/doc/sequence.html # Note the lack of any white space between names 2 and 3 and their seqs. with open(path) as stream: alignments = Align.parse(stream, "phylip") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'A', 'G', 'C', 'T', 'N', 'G', 'G', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'T', 'G', 'A', 'G', 'C', 'C', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'T', 'A', 'C', 'A', 'G', 'G', 'G', 'T', 'A', 'T'], ['A', 'A', 'G', 'C', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G', 'T', 'G', 'C', 'A', 'G', 'G', 'G', 'T', 'G', 'A', 'G', 'C', 'C', 'G', 'T', 'G', 'G', 'C', 'C', 'G', 'G', 'G', 'C', 'A', 'C', 'G', 'G', 'T', 'A', 'T'], ['A', 'C', 'C', 'G', 'G', 'T', 'T', 'G', 'G', 'C', 'C', 'G', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'T', 'A', 'C', 'A', 'G', 'G', 'T', 'T', 'G', 'G', 'C', 'C', 'G', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'T', 'A', 'A'], ['A', 'A', 'A', 'C', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'G', 'T', 'T', 'A', 'C', 'G', 'C', 'T', 'T', 'A', 'A', 'A', 'C', 'C', 'G', 'A', 'G', 'G', 'C', 'C', 'G', 'G', 'G', 'A', 'C', 'A', 'C', 'T', 'C', 'A', 'T'], ['A', 'A', 'A', 'C', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'G', 'G', 'T', 'A', 'C', 'G', 'C', 'T', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'T', 'T', 'G', 'C', 'C', 'G', 'G', 'T', 'A', 'C', 'G', 'C', 'T', 'T', 'A', 'A']], dtype='U') # fmt: on ) ) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 5) self.assertEqual(alignment.sequences[0].id, "Turkey") self.assertEqual(alignment.sequences[1].id, "Salmo gair") self.assertEqual(alignment.sequences[2].id, "H. Sapiens") self.assertEqual(alignment.sequences[3].id, "Chimp") self.assertEqual(alignment.sequences[4].id, "Gorilla") self.assertEqual( alignment.sequences[0].seq, "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT" ) self.assertEqual( alignment.sequences[1].seq, "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT" ) self.assertEqual( alignment.sequences[2].seq, "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA" ) self.assertEqual( alignment.sequences[3].seq, "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT" ) self.assertEqual( alignment.sequences[4].seq, "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA" ) self.assertEqual(alignment[0], "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT") self.assertEqual(alignment[1], "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT") self.assertEqual(alignment[2], "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA") self.assertEqual(alignment[3], "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT") self.assertEqual(alignment[4], "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA") self.check_reading_writing(path) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 42], [0, 42], [0, 42], [0, 42], [0, 42]]), ) ) self.assertEqual( str(alignment), """\ Turkey 0 AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT 42 Salmo gai 0 AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT 42 H. Sapien 0 ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA 42 Chimp 0 AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT 42 Gorilla 0 AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA 42 """, ) self.assertEqual( format(alignment, "phylip"), """\ 5 42 Turkey AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT Salmo gairAAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT H. SapiensACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Chimp AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT Gorilla AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA """, ) def test_five_and_six(self): paths = ("Phylip/five.dat", "Phylip/six.dat") # http://evolution.genetics.washington.edu/phylip/doc/sequence.html for path in paths: with open(path) as stream: alignments = Align.parse(stream, "phylip") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 5) self.assertEqual(alignment.sequences[0].id, "Turkey") self.assertEqual(alignment.sequences[1].id, "Salmo gair") self.assertEqual(alignment.sequences[2].id, "H. Sapiens") self.assertEqual(alignment.sequences[3].id, "Chimp") self.assertEqual(alignment.sequences[4].id, "Gorilla") self.assertEqual( alignment.sequences[0].seq, "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT" ) self.assertEqual( alignment.sequences[1].seq, "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT" ) self.assertEqual( alignment.sequences[2].seq, "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA" ) self.assertEqual( alignment.sequences[3].seq, "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT" ) self.assertEqual( alignment.sequences[4].seq, "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA" ) self.assertEqual(alignment[0], "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT") self.assertEqual(alignment[1], "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT") self.assertEqual(alignment[2], "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA") self.assertEqual(alignment[3], "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT") self.assertEqual(alignment[4], "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA") self.assertEqual( str(alignment), """\ Turkey 0 AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT 42 Salmo gai 0 AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT 42 H. Sapien 0 ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA 42 Chimp 0 AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT 42 Gorilla 0 AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA 42 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 42], [0, 42], [0, 42], [0, 42], [0, 42]]), ) ) self.assertEqual( format(alignment, "phylip"), """\ 5 42 Turkey AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT Salmo gairAAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT H. SapiensACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Chimp AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT Gorilla AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA """, ) self.check_reading_writing(path) def test_interlaced(self): path = "Phylip/interlaced.phy" with open(path) as stream: alignments = Align.parse(stream, "phylip") self.check_sequential_interlaced(alignments) alignments = iter(alignments) self.check_sequential_interlaced(alignments) with Align.parse(path, "phylip") as alignments: self.check_sequential_interlaced(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "phylip") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def test_sequential(self): path = "Phylip/sequential.phy" with open(path) as stream: alignments = Align.parse(stream, "phylip") self.check_sequential_interlaced(alignments) alignments = iter(alignments) self.check_sequential_interlaced(alignments) with Align.parse(path, "phylip") as alignments: self.check_sequential_interlaced(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "phylip") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def check_sequential_interlaced(self, alignments): alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 3) self.assertEqual(alignment.sequences[0].id, "CYS1_DICDI") self.assertEqual(alignment.sequences[1].id, "ALEU_HORVU") self.assertEqual(alignment.sequences[2].id, "CATH_HUMAN") self.assertEqual( alignment.sequences[0].seq, "MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII", ) self.assertEqual( alignment.sequences[1].seq, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA", ) self.assertEqual( alignment.sequences[2].seq, "MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNNGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV", ) self.assertEqual( alignment[0], "-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII--", ) self.assertEqual( alignment[1], "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEEFQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA", ) self.assertEqual( alignment[2], "------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FHFKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV", ) self.assertEqual( str(alignment), """\ CYS1_DICD 0 -----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQ ALEU_HORV 0 MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALR CATH_HUMA 0 ------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FH CYS1_DICD 28 FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE ALEU_HORV 60 FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEE CATH_HUMA 34 FKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAE CYS1_DICD 87 FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFS ALEU_HORV 116 FQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFS CATH_HUMA 89 IKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFS CYS1_DICD 146 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG ALEU_HORV 172 TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG CATH_HUMA 145 TTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNK CYS1_DICD 206 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAV ALEU_HORV 224 GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI CATH_HUMA 197 GIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT CYS1_DICD 265 E-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG ALEU_HORV 283 DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNG CATH_HUMA 256 QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNG CYS1_DICD 321 YIYLRRGKNTCGVSNFVSTSII-- 343 ALEU_HORV 338 YFKMEMGKNMCAIATCASYPVVAA 362 CATH_HUMA 311 YFLIERGKNMCGLAACASYPIPLV 335 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array( [[ 0, 0, 1, 18, 18, 18, 26, 26, 40, 40, 63, 67, 93, 94, 103, 105, 113, 115, 128, 128, 180, 188, 222, 223, 242, 242, 266, 266, 275, 275, 280, 280, 299, 304, 343, 343], [ 0, 5, 6, 23, 31, 38, 46, 58, 72, 73, 96, 96, 122, 122, 131, 133, 141, 141, 154, 154, 206, 206, 240, 240, 259, 260, 284, 285, 294, 295, 300, 302, 321, 321, 360, 362], [ 0, 0, 0, 17, 17, 24, 32, 32, 46, 46, 69, 69, 95, 96, 105, 105, 113, 113, 126, 127, 179, 179, 213, 213, 232, 233, 257, 258, 267, 268, 273, 275, 294, 294, 333, 335]]) # fmt: on ) ) self.assertEqual( format(alignment, "phylip"), """\ 3 384 CYS1_DICDI-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII-- ALEU_HORVUMAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEEFQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA CATH_HUMAN------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FHFKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV """, ) def test_interlaced2(self): path = "Phylip/interlaced2.phy" with open(path) as stream: alignments = Align.parse(stream, "phylip") self.check_sequential_interlaced2(alignments) alignments = iter(alignments) self.check_sequential_interlaced2(alignments) with Align.parse(path, "phylip") as alignments: self.check_sequential_interlaced2(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "phylip") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def test_sequential2(self): path = "Phylip/sequential2.phy" with open(path) as stream: alignments = Align.parse(stream, "phylip") self.check_sequential_interlaced2(alignments) alignments = iter(alignments) self.check_sequential_interlaced2(alignments) with Align.parse(path, "phylip") as alignments: self.check_sequential_interlaced2(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "phylip") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def check_sequential_interlaced2(self, alignments): alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 4) self.assertEqual(alignment.sequences[0].id, "IXI_234") self.assertEqual(alignment.sequences[1].id, "IXI_235") self.assertEqual(alignment.sequences[2].id, "IXI_236") self.assertEqual(alignment.sequences[3].id, "IXI_237") self.assertEqual( alignment.sequences[0].seq, "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[1].seq, "TSPASIRPPAGPSSRRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[2].seq, "TSPASIRPPAGPSSRPAMVSSRRPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRGSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE", ) self.assertEqual( alignment.sequences[3].seq, "TSPASLRPPAGPSSRPAMVSSRRRPSPPGPRRPTCSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSRGSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE", ) self.assertEqual( alignment[0], "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[1], "TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[2], "TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE", ) self.assertEqual( alignment[3], "TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE", ) self.assertEqual( str(alignment), """\ IXI_234 0 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC IXI_235 0 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC IXI_236 0 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTC IXI_237 0 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTC IXI_234 60 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG IXI_235 51 TTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG IXI_236 58 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTG IXI_237 55 TTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTG IXI_234 120 PPAWAGDRSHE 131 IXI_235 101 PPAWAGDRSHE 112 IXI_236 116 PPPPAGDRSHE 127 IXI_237 113 PPAYAGDRSHE 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 15, 22, 23, 24, 35, 39, 74, 84, 97, 99, 131], [0, 15, 15, 15, 15, 26, 30, 65, 65, 78, 80, 112], [0, 15, 22, 22, 22, 33, 37, 72, 82, 95, 95, 127], [0, 15, 22, 23, 23, 34, 34, 69, 79, 92, 92, 124]]) # fmt: on ) ) self.assertEqual( format(alignment, "phylip"), """\ 4 131 IXI_234 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE IXI_235 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE IXI_236 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE IXI_237 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE """, ) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)