# Copyright 2006-2014 by Peter Cock. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Bio.Align.clustal module.""" import unittest from io import StringIO import numpy as np from Bio import Align class TestClustalReadingWriting(unittest.TestCase): def check_reading_writing(self, path): alignments = Align.parse(path, "clustal") stream = StringIO() n = Align.write(alignments, stream, "clustal") self.assertEqual(n, 1) alignments = Align.parse(path, "clustal") alignment = next(alignments) stream.seek(0) saved_alignments = Align.parse(stream, "clustal") self.assertEqual(saved_alignments.metadata, alignments.metadata) 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]) def test_clustalw(self): path = "Clustalw/clustalw.aln" # includes the sequence length on the right hand side of each line with open(path) as stream: alignments = Align.parse(stream, "clustal") self.check_clustalw(alignments) alignments = iter(alignments) self.check_clustalw(alignments) with Align.parse(path, "clustal") as alignments: self.check_clustalw(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "clustal") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def check_clustalw(self, alignments): self.assertEqual(alignments.metadata["Program"], "CLUSTAL") self.assertEqual(alignments.metadata["Version"], "1.81") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.sequences[0].id, "gi|4959044|gb|AAD34209.1|AF069") self.assertEqual(alignment.sequences[1].id, "gi|671626|emb|CAA85685.1|") self.assertEqual( alignment.sequences[0].seq, "MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNSESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV", ) self.assertEqual( alignment.sequences[1].seq, "MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD", ) self.assertEqual( alignment[0], "MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNSESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESVV", ) self.assertEqual( alignment[1], "---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPG-----------------VPPEEAGAAVAAESSTGT---------WTTVWTDGLTSLDRYKG-----RCYHIEPVPG-------------------EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAG-----------------------TCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVIPVASG-----------------------------GIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACVKARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD---", ) self.assertEqual( str(alignment), """\ gi|495904 0 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE 0 ---------.|.|..............|.............|............||---- gi|671626 0 ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPG---- gi|495904 60 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS 60 -------------.||.......|.|||...---------...|...|.|...|..|--- gi|671626 47 -------------VPPEEAGAAVAAESSTGT---------WTTVWTDGLTSLDRYKG--- gi|495904 120 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSAS 120 --......|..|-------------------|...............|..|...|..|.. gi|671626 82 --RCYHIEPVPG-------------------EKDQCICYVAYPLDLFEEGSVTNMFTSIV gi|495904 180 ESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRR 180 ....................|................|.......|.............. gi|671626 121 GNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLS gi|495904 240 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS 240 |............|.....................|.||.|.........|......... gi|671626 181 AKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN gi|495904 300 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF 300 ...|-----------------------.......|...........|......|||.... gi|671626 241 ATAG-----------------------TCEEMIKRAIFARELGVPIVMHDYLTGGFTANT gi|495904 360 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMYSDSDSE 360 |.............|.............................|....|.........| gi|671626 278 SLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGE gi|495904 420 PSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGS 420 ...........|........|.|........|.....|..||------------------ gi|671626 338 RDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVIPVASG------------------ gi|495904 480 SGPSRKDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGEN 480 -----------.............|...............|.|.......|...------ gi|671626 380 -----------GIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA------ gi|495904 540 DALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESV 540 -----...|.....||---|.|.............|..|-...|..............-- gi|671626 423 -----VEACVKARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD-- gi|495904 599 V 600 600 - 601 gi|671626 473 - 473 """, ) self.assertEqual( format(alignment, "clustal"), """\ gi|4959044|gb|AAD34209.1|AF069 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN gi|671626|emb|CAA85685.1| ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFR * *: :: :. :* : :. : . :* :: . gi|4959044|gb|AAD34209.1|AF069 LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW gi|671626|emb|CAA85685.1| VTPQPG-----------------VPPEEAGAAVAAESSTGT--------- : ** **:... *.*** .. gi|4959044|gb|AAD34209.1|AF069 LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT gi|671626|emb|CAA85685.1| WTTVWTDGLTSLDRYKG-----RCYHIEPVPG------------------ .:* * *: .* :* : :* .* gi|4959044|gb|AAD34209.1|AF069 SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE gi|671626|emb|CAA85685.1| -EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP *::. . .:: :*..* :* .* .. . : . : gi|4959044|gb|AAD34209.1|AF069 VPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSEN gi|671626|emb|CAA85685.1| VAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE *. .:: : . .* . : *.: ..:: * . :: : gi|4959044|gb|AAD34209.1|AF069 EPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS gi|671626|emb|CAA85685.1| CLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN .*. :. :. . . .* **.*.. :.. *.. . . gi|4959044|gb|AAD34209.1|AF069 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYE gi|671626|emb|CAA85685.1| ATAG-----------------------TCEEMIKRAIFARELGVPIVMHD ::* :.: .*: : * :: gi|4959044|gb|AAD34209.1|AF069 SERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLR gi|671626|emb|CAA85685.1| YLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKAL *** . * :. . . : *: .:: ::: .. . : : gi|4959044|gb|AAD34209.1|AF069 QIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGS gi|671626|emb|CAA85685.1| RLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDW :: * * : .. :.* . ::. :: * : : * * :.. gi|4959044|gb|AAD34209.1|AF069 SSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESG gi|671626|emb|CAA85685.1| VSLPGVIPVASG-----------------------------GIHVWHMPA * .. * :** . .:. .. gi|4959044|gb|AAD34209.1|AF069 SLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCI gi|671626|emb|CAA85685.1| LTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACV :*. ..: :. . .:* * : : * . ..*: gi|4959044|gb|AAD34209.1|AF069 TEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESV gi|671626|emb|CAA85685.1| KARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD-- . .** *.*... : :: :* .* ::* : :. :. : gi|4959044|gb|AAD34209.1|AF069 V gi|671626|emb|CAA85685.1| - """, # noqa: W293 ) def test_msaprobs(self): path = "Clustalw/msaprobs.aln" # This example was obtained from # http://virgil.ruc.dk/kurser/Sekvens/Treedraw.htm with open(path) as stream: alignments = Align.parse(stream, "clustal") self.assertEqual(alignments.metadata["Program"], "MSAPROBS") self.assertEqual(alignments.metadata["Version"], "0.9.7") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 8) self.assertEqual(alignment.shape, (8, 298)) self.assertEqual(alignment.sequences[0].id, "V_Harveyi_PATH") self.assertEqual(alignment.sequences[1].id, "B_subtilis_YXEM") self.assertEqual(alignment.sequences[2].id, "FLIY_ECOLI") self.assertEqual(alignment.sequences[3].id, "Deinococcus_radiodurans") self.assertEqual(alignment.sequences[4].id, "B_subtilis_GlnH_homo_YCKK") self.assertEqual(alignment.sequences[5].id, "YA80_HAEIN") self.assertEqual(alignment.sequences[6].id, "E_coli_GlnH") self.assertEqual(alignment.sequences[7].id, "HISJ_E_COLI") self.assertEqual( alignment.sequences[0].seq, "MKNWIKVAVAAIALSAATVQAATEVKVGMSGRYFPFTFVKQDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDTGIEHDVALGRADAFIMDRLSALELIKKTGLPLQLAGEPFETIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK", ) self.assertEqual( alignment.sequences[1].seq, "MKMKKWTVLVVAALLAVLSACGNGNSSSKEDDNVLHVGATGQSYPFAYKENGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIAQIKKTGLPLKLAGDPIVYEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH", ) self.assertEqual( alignment.sequences[2].seq, "MKLAHLGRQALMGVMAVALVAGMSVKSFADEGLLNKVKERGTLLVGLEGTYPPFSFQGDDGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVTGEAFSRQESGVALRKGNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK", ) self.assertEqual( alignment.sequences[3].seq, "MKKSLLSLKLSGLLVPSVLALSLSACSSPSSTLNQGTLKIAMEGTYPPFTSKNEQGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTGDIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNYIINDQKLPVRGAGQIGDAAPVGIALKKGNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP", ) self.assertEqual( alignment.sequences[4].seq, "MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVGKTDREDKYDFSDKYTTSRAVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATNAGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLNYLKTSGNKNVKIAFETGEPQSTYFTFRKGSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK", ) self.assertEqual( alignment.sequences[5].seq, "MKKLLFTTALLTGAIAFSTFSHAGEIADRVEKTKTLLVGTEGTYAPFTFHDKSGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKAAGAQILVVDGLAQSLELIKQGRAEATINDKLAVLDYFKQHPNSGLKIAYDRGDKTPTAFAFLQGEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ", ) self.assertEqual( alignment.sequences[6].seq, "MKSVLKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK", ) self.assertEqual( alignment.sequences[7].seq, "MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG", ) self.assertEqual( alignment[0], "MKNW--------IKV----AVAAI-A--LSAA-------------------TVQAATEVKVGMSGRYFPFTFVK--QDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRK-GNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKTG-LPLQLAGEPFE-----TIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK----", ) self.assertEqual( alignment[1], "MKMKKW------TVL----VVAALLA-VLSACGN------------G-NSSSKEDDNVLHVGATGQSYPFAYKE--NGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKK-DNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKTG-LPLKLAGDPIV-----YEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH", ) self.assertEqual( alignment[2], "MKLAHLGRQALMGVM----AVALVAG--MSVKSF---------ADEG-LLNKVKERGTLLVGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQN--VQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKTN-DTLAVTGEAFS-----RQESGVALRK--GNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK----", ) self.assertEqual( alignment[3], "MKKSLL------SLKLSGLLVPSVLALSLSACSS---------------PSSTLNQGTLKIAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLI-D--TGDIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNY-IIND-QKLPVRGAGQIGD-----AAPVGIALKK--GNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQ---P", ) self.assertEqual( alignment[4], "MKKALL------ALF----MVVSIAA--LAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVGKTD-REDKYDFSDKYTTSRAVVVTKK-DNNDIKSEADVKGKTSAQSLTSNYNKLAT-N--A-GAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGE-----PQSTYFTFRK--GSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK----", ) self.assertEqual( alignment[5], "MKKLLF------TTA----LLTGAIA--FSTFS-----------HAGEIADRVEKTKTLLVGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKS-SDNSIKSFEDLKGRKSAQSATSNWGKDAK-A--A-GAQILVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGD-----KTPTAFAFLQ--GEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ----", ) self.assertEqual( alignment[6], "MKSVL-------KVS----LAALTLA--FAVSSH---------A----------ADKKLVVATDTAFVPFEFKQ--GDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKAN-NNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLE-----AQQYGIAFPK--GSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP-K----", ) self.assertEqual( alignment[7], "MKKLVL------SLS----LV---LA--FSSATA---------------A-FAAIPQNIRIGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK-NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRK--EDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYG---G", ) self.assertEqual( alignment.column_annotations["clustal_consensus"], "** . :: *. *: : :. ** . .: *::::. : :. . ..: *.: . * : * *: . .. .: *: . : .: : * : . .: : .:: : .: .: :: :** . : ::*. : ", ) self.assertEqual( str(alignment), """\ V_Harveyi 0 MKNW--------IKV----AVAAI-A--LSAA-------------------TVQAATEVK B_subtili 0 MKMKKW------TVL----VVAALLA-VLSACGN------------G-NSSSKEDDNVLH FLIY_ECOL 0 MKLAHLGRQALMGVM----AVALVAG--MSVKSF---------ADEG-LLNKVKERGTLL Deinococc 0 MKKSLL------SLKLSGLLVPSVLALSLSACSS---------------PSSTLNQGTLK B_subtili 0 MKKALL------ALF----MVVSIAA--LAACGAGNDNQSKDNAKDGDLWASIKKKGVLT YA80_HAEI 0 MKKLLF------TTA----LLTGAIA--FSTFS-----------HAGEIADRVEKTKTLL E_coli_Gl 0 MKSVL-------KVS----LAALTLA--FAVSSH---------A----------ADKKLV HISJ_E_CO 0 MKKLVL------SLS----LV---LA--FSSATA---------------A-FAAIPQNIR V_Harveyi 26 VGMSGRYFPFTFVK--QDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDT B_subtili 36 VGATGQSYPFAYKE--NGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDT FLIY_ECOL 44 VGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDV Deinococc 39 IAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDV B_subtili 48 VGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDV YA80_HAEI 37 VGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDV E_coli_Gl 28 VATDTAFVPFEFKQ--GDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDL HISJ_E_CO 29 IGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDA V_Harveyi 84 ISNQITMTDARKAKYLFADPYVVDGAQITVRK-GNDSIQGVEDLAGKTVAVNLGSNFEQL B_subtili 94 ISNQVAVTDERKETYNFTKPYAYAGTQIVVKK-DNTDIKSVDDLKGKTVAAVLGSNHAKN FLIY_ECOL 103 VINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEW Deinococc 98 IVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQ B_subtili 108 VANQVGKTD-REDKYDFSDKYTTSRAVVVTKK-DNNDIKSEADVKGKTSAQSLTSNYNKL YA80_HAEI 96 IANQTNPSPERLKKYSFTTPYNYSGGVIVTKS-SDNSIKSFEDLKGRKSAQSATSNWGKD E_coli_Gl 86 ALAGITITDERKKAIDFSDGYYKSGLLVMVKAN-NNDVKSVKDLDGKVVAVKSGTGSVDY HISJ_E_CO 88 IMSSLSITEKRQQEIAFTDKLYAADSRLVVAK-NSDIQPTVESLKGKRVGVLQGTTQETF V_Harveyi 143 LRDYDKDGKINIKTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKTG-LPLQLAGEPF B_subtili 153 LESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKTG-LPLKLAGDPI FLIY_ECOL 163 LRQN--VQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKTN-DTLAVTGEAF Deinococc 158 LI-D--TGDIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNY-IIND-QKLPVRGAGQIG B_subtili 166 AT-N--A-GAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETG YA80_HAEI 155 AK-A--A-GAQILVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRG E_coli_Gl 145 AKAN--IKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSL HISJ_E_CO 147 GNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSV V_Harveyi 199 E-----TIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK---- B_subtili 211 V-----YEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH FLIY_ECOL 219 S-----RQESGVALRK--GNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK---- Deinococc 213 D-----AAPVGIALKK--GNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQ---P B_subtili 221 E-----PQSTYFTFRK--GSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK---- YA80_HAEI 210 D-----KTPTAFAFLQ--GEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ---- E_coli_Gl 202 E-----AQQYGIAFPK--GSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP-K---- HISJ_E_CO 207 KDEKLFGVGTGMGLRK--EDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYG---G V_Harveyi 248 B_subtili 264 FLIY_ECOL 266 Deinococc 261 B_subtili 268 YA80_HAEI 257 E_coli_Gl 248 HISJ_E_CO 260 """, ) self.assertEqual( format(alignment, "clustal"), """\ V_Harveyi_PATH MKNW--------IKV----AVAAI-A--LSAA------------------ B_subtilis_YXEM MKMKKW------TVL----VVAALLA-VLSACGN------------G-NS FLIY_ECOLI MKLAHLGRQALMGVM----AVALVAG--MSVKSF---------ADEG-LL Deinococcus_radiodurans MKKSLL------SLKLSGLLVPSVLALSLSACSS---------------P B_subtilis_GlnH_homo_YCKK MKKALL------ALF----MVVSIAA--LAACGAGNDNQSKDNAKDGDLW YA80_HAEIN MKKLLF------TTA----LLTGAIA--FSTFS-----------HAGEIA E_coli_GlnH MKSVL-------KVS----LAALTLA--FAVSSH---------A------ HISJ_E_COLI MKKLVL------SLS----LV---LA--FSSATA---------------A ** . :: *. *: V_Harveyi_PATH -TVQAATEVKVGMSGRYFPFTFVK--QDKLQGFEVDMWDEIGKRNDYKIE B_subtilis_YXEM SSKEDDNVLHVGATGQSYPFAYKE--NGKLTGFDVEVMEAVAKKIDMKLD FLIY_ECOLI NKVKERGTLLVGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEAS Deinococcus_radiodurans SSTLNQGTLKIAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPE B_subtilis_GlnH_homo_YCKK ASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVD YA80_HAEIN DRVEKTKTLLVGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVE E_coli_GlnH ----ADKKLVVATDTAFVPFEFKQ--GDKYVGFDVDLWAAIAKELKLDYE HISJ_E_COLI -FAAIPQNIRIGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCT : :. ** . .: *::::. : :. . V_Harveyi_PATH YVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITV B_subtilis_YXEM WKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVV FLIY_ECOLI LKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALV Deinococcus_radiodurans FVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIV B_subtilis_GlnH_homo_YCKK FKETQWGSMFAGLNSKRFDVVANQVGKTD-REDKYDFSDKYTTSRAVVVT YA80_HAEIN FKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVT E_coli_GlnH LKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMV HISJ_E_COLI FVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVV ..: *.: . * : * *: . V_Harveyi_PATH RK-GNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT--G B_subtilis_YXEM KK-DNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEG FLIY_ECOLI KKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQN--VQGVDVRTYDDDPT Deinococcus_radiodurans AKNNTFNPQSLADLKGKRVGSTLGSNYEKQLI-D--TGDIKIVTYPGAPE B_subtilis_GlnH_homo_YCKK KK-DNNDIKSEADVKGKTSAQSLTSNYNKLAT-N--A-GAKVEGVEGMAQ YA80_HAEIN KS-SDNSIKSFEDLKGRKSAQSATSNWGKDAK-A--A-GAQILVVDGLAQ E_coli_GlnH KAN-NNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNIDN HISJ_E_COLI AK-NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDN .. .: *: . : .: V_Harveyi_PATH IEHDVALGRADAFIMDRLSALE-LIKKTG-LPLQLAGEPFE-----TIQN B_subtilis_YXEM TLKDVAYGRVDAYVNSRTVLIA-QIKKTG-LPLKLAGDPIV-----YEQV FLIY_ECOLI KYQDLRVGRIDAILVDRLAALD-LVKKTN-DTLAVTGEAFS-----RQES Deinococcus_radiodurans ILADLVAGRIDAAYNDRLVVNY-IIND-QKLPVRGAGQIGD-----AAPV B_subtilis_GlnH_homo_YCKK ALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGE-----PQST YA80_HAEIN SLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGD-----KTPT E_coli_GlnH AYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLE-----AQQY HISJ_E_COLI IYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGT : * : . .: V_Harveyi_PATH AWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK---- B_subtilis_YXEM AFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH FLIY_ECOLI GVALRK--GNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK---- Deinococcus_radiodurans GIALKK--GNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQ---P B_subtilis_GlnH_homo_YCKK YFTFRK--GSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK---- YA80_HAEIN AFAFLQ--GEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ---- E_coli_GlnH GIAFPK--GSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP-K---- HISJ_E_COLI GMGLRK--EDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYG---G : .:: : .: .: :: :** . : ::*. : """, ) self.check_reading_writing(path) def test_muscle(self): path = "Clustalw/muscle.aln" # includes the sequence length on the right hand side of each line with open(path) as stream: alignments = Align.parse(stream, "clustal") self.assertEqual(alignments.metadata["Program"], "MUSCLE") self.assertEqual(alignments.metadata["Version"], "3.8") 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, "Test1seq") self.assertEqual(alignment.sequences[1].id, "AT3G20900.1-SEQ") self.assertEqual(alignment.sequences[2].id, "AT3G20900.1-CDS") self.assertEqual( alignment.sequences[0].seq, "AGTTACAATAACTGACGAAGCTAAGTAGGCTACTAATTAACGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGTAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATCGTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACAAAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAACGTAAACAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTTCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACGGTCGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTT", ) self.assertEqual( alignment.sequences[1].seq, "ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAACAAAAAAAAAACTCAATCCACATCAAAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAAATTAAAGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGCAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATAGTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAACAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAAAAAAAAAAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTGCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG", ) self.assertEqual( alignment.sequences[2].seq, "ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG", ) self.assertEqual( alignment[0], "-----------------------------------------------------------------AGTTACAATAACTGACGAAGCTAAGTAGGCTACTAATTAACGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGTAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATCGTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACAAAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAACGTAAACAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTTCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACGGTCGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTT-", ) self.assertEqual( alignment[1], "ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAACAAAAAAAAAACTCAATCCACATCAAAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAAATTAAAGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGCAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATAGTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAACAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAAAAAAAAAAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTGCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG", ) self.assertEqual( alignment[2], "--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGAACAAAGTAGCGAGGAAGAA------------------------------CAAAACATC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG", ) self.assertEqual( alignment.column_annotations["clustal_consensus"], " ***** *** ** * ** * ******** *********************************** ** * **** ******************************************************************************* ******************************************** ", ) self.assertEqual( str(alignment), """\ Test1seq 0 ------------------------------------------------------------ AT3G20900 0 ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAACAAAAAAAAAACTCAATCCAC AT3G20900 0 ------------------------------------------------------------ Test1seq 0 -----AGTTACAATAACTGACGAAGCTAAGTAGGCTACTAATTAACGTCATCAACCTAAT AT3G20900 60 ATCAAAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAAATTAAAGTCATCAACCTAAT AT3G20900 0 ------------------------------------------------------------ Test1seq 55 ACATAGCACTTAGAAAAAAGTGAAGTAAGAAAATATAAAATAATAAAAGGGTGGGTTATC AT3G20900 120 ACATAGCACTTAGAAAAAAGTGAAGCAAGAAAATATAAAATAATAAAAGGGTGGGTTATC AT3G20900 0 ------------------------------------------------------------ Test1seq 115 AATTGATAGTGTAAATCATCGTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGA AT3G20900 180 AATTGATAGTGTAAATCATAGTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGA AT3G20900 0 ------------------------------------------------------------ Test1seq 175 CTTGATTCAAATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACA AT3G20900 240 CTTGATTCAAATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAA AT3G20900 0 --------------------------------------ATGAACAAAGTAGCGAGGAAGA Test1seq 235 AAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATT AT3G20900 300 CAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATT AT3G20900 22 A------------------------------CAAAACATC-------------------- Test1seq 295 GTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGAT AT3G20900 360 GTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGAT AT3G20900 32 ------------------------------------------------------------ Test1seq 355 CCTATATCAACGTAAACAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGT AT3G20900 420 CCTATATCAAAAAAAAAAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGT AT3G20900 32 ------------------------------------------------------------ Test1seq 415 TCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGT AT3G20900 480 GCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGT AT3G20900 32 --------------------------------AGCAAAGAAAACGATCTGTCTCCGTCGT Test1seq 475 AACACACGGTCGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC AT3G20900 540 AACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC AT3G20900 60 AACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC Test1seq 535 GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGTCAGCACCGCT AT3G20900 600 GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCT AT3G20900 120 GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCT Test1seq 595 GCTGGGGATGGAGAGGGAACAGAGTT- 621 AT3G20900 660 GCTGGGGATGGAGAGGGAACAGAGTAG 687 AT3G20900 180 GCTGGGGATGGAGAGGGAACAGAGTAG 207 """, ) self.assertEqual( format(alignment, "clustal"), """\ Test1seq -------------------------------------------------- AT3G20900.1-SEQ ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAACAAAAAAAAAA AT3G20900.1-CDS -------------------------------------------------- Test1seq ---------------AGTTACAATAACTGACGAAGCTAAGTAGGCTACTA AT3G20900.1-SEQ CTCAATCCACATCAAAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAA AT3G20900.1-CDS -------------------------------------------------- Test1seq ATTAACGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGTAAGA AT3G20900.1-SEQ ATTAAAGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGCAAGA AT3G20900.1-CDS -------------------------------------------------- Test1seq AAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATC AT3G20900.1-SEQ AAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATA AT3G20900.1-CDS -------------------------------------------------- Test1seq GTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAA AT3G20900.1-SEQ GTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAA AT3G20900.1-CDS -------------------------------------------------- Test1seq ATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACA AT3G20900.1-SEQ ATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAA AT3G20900.1-CDS ----------------------------ATGAACAAAGTAGCGAGGAAGA ***** *** ** * ** * Test1seq AAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACT AT3G20900.1-SEQ CAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACT AT3G20900.1-CDS A------------------------------CAAAACATC---------- ******** Test1seq CTTCGTTATTGTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTA AT3G20900.1-SEQ CTTCGTTATTGTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTA AT3G20900.1-CDS -------------------------------------------------- Test1seq ATACTACTTTCTGTATTGATCCTATATCAACGTAAACAAAGATACTAATA AT3G20900.1-SEQ ATACTACTTTCTGTATTGATCCTATATCAAAAAAAAAAAAGATACTAATA AT3G20900.1-CDS -------------------------------------------------- Test1seq ATTAACTAAAAGTACGTTCATCGATCGTGTTCGTTGACGAAGAAGAGCTC AT3G20900.1-SEQ ATTAACTAAAAGTACGTTCATCGATCGTGTGCGTTGACGAAGAAGAGCTC AT3G20900.1-CDS -------------------------------------------------- Test1seq TATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACGGT AT3G20900.1-SEQ TATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGT AT3G20900.1-CDS ------------AGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGT *********************************** ** Test1seq CGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC AT3G20900.1-SEQ TTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC AT3G20900.1-CDS TTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC * **** *************************************** Test1seq GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGT AT3G20900.1-SEQ GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGT AT3G20900.1-CDS GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGT **************************************** ********* Test1seq CAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTT- AT3G20900.1-SEQ CAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG AT3G20900.1-CDS CAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAG *********************************** """, # noqa: W293 ) self.check_reading_writing(path) def test_kalign(self): """Make sure we can parse the Kalign header.""" path = "Clustalw/kalign.aln" with open(path) as stream: alignments = Align.parse(stream, "clustal") self.assertEqual(alignments.metadata["Program"], "Kalign") self.assertEqual(alignments.metadata["Version"], "2.0") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'C', 'T', 'G', 'G', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'G', 'A', 'G', 'T', '-', 'T'], ['G', 'C', 'T', 'G', 'G', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'G', 'A', 'G', 'T', 'A', 'G'] ], dtype='U') # fmt: on ) ) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.sequences[0].id, "Test1seq") self.assertEqual(alignment.sequences[1].id, "AT3G20900") self.assertEqual(alignment.sequences[0].seq, "GCTGGGGATGGAGAGGGAACAGAGTT") self.assertEqual(alignment.sequences[1].seq, "GCTGGGGATGGAGAGGGAACAGAGTAG") self.assertEqual(alignment[0], "GCTGGGGATGGAGAGGGAACAGAGT-T") self.assertEqual(alignment[1], "GCTGGGGATGGAGAGGGAACAGAGTAG") self.assertEqual( str(alignment), """\ Test1seq 0 GCTGGGGATGGAGAGGGAACAGAGT-T 26 0 |||||||||||||||||||||||||-. 27 AT3G20900 0 GCTGGGGATGGAGAGGGAACAGAGTAG 27 """, ) self.assertEqual( format(alignment, "clustal"), """\ Test1seq GCTGGGGATGGAGAGGGAACAGAGT-T AT3G20900 GCTGGGGATGGAGAGGGAACAGAGTAG """, ) self.check_reading_writing(path) def test_probcons(self): path = "Clustalw/probcons.aln" # example taken from the PROBCONS documentation with open(path) as stream: alignments = Align.parse(stream, "clustal") self.assertEqual(alignments.metadata["Program"], "PROBCONS") self.assertEqual(alignments.metadata["Version"], "1.12") alignment = next(alignments) with self.assertRaises(StopIteration): next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['D', '-', 'V', 'L', 'L', 'G', 'A', 'N', 'G', 'G', 'V', 'L', 'V', 'F', 'E', 'P', 'N', 'D', 'F', 'S', 'V', 'K', 'A', 'G', 'E', 'T', 'I', 'T', 'F', 'K', 'N', 'N', 'A', 'G', 'Y', 'P', 'H', 'N', 'V', 'V', 'F', 'D', 'E', 'D', 'A', 'V', 'P', 'S', 'G', '-', 'V', 'D', '-', 'V', 'S', 'K', 'I', 'S', 'Q', 'E', 'E', 'Y', 'L', 'T', 'A', 'P', 'G', 'E', 'T', 'F', 'S', 'V', 'T', 'L', 'T', 'V', '-', '-', '-', 'P', 'G', 'T', 'Y', 'G', 'F', 'Y', 'C', 'E', 'P', 'H', 'A', 'G', 'A', 'G', 'M', 'V', 'G', 'K', 'V', 'T', 'V'], ['-', '-', 'V', 'K', 'L', 'G', 'A', 'D', 'S', 'G', 'A', 'L', 'E', 'F', 'V', 'P', 'K', 'T', 'L', 'T', 'I', 'K', 'S', 'G', 'E', 'T', 'V', 'N', 'F', 'V', 'N', 'N', 'A', 'G', 'F', 'P', 'H', 'N', 'I', 'V', 'F', 'D', 'E', 'D', 'A', 'I', 'P', 'S', 'G', '-', 'V', 'N', '-', 'A', 'D', 'A', 'I', 'S', 'R', 'D', 'D', 'Y', 'L', 'N', 'A', 'P', 'G', 'E', 'T', 'Y', 'S', 'V', 'K', 'L', 'T', 'A', '-', '-', '-', 'A', 'G', 'E', 'Y', 'G', 'Y', 'Y', 'C', 'E', 'P', 'H', 'Q', 'G', 'A', 'G', 'M', 'V', 'G', 'K', 'I', 'I', 'V'], ['-', '-', 'V', 'K', 'L', 'G', 'S', 'D', 'K', 'G', 'L', 'L', 'V', 'F', 'E', 'P', 'A', 'K', 'L', 'T', 'I', 'K', 'P', 'G', 'D', 'T', 'V', 'E', 'F', 'L', 'N', 'N', 'K', 'V', 'P', 'P', 'H', 'N', 'V', 'V', 'F', 'D', 'A', 'A', 'L', 'N', 'P', 'A', 'K', 'S', 'A', 'D', 'L', 'A', 'K', 'S', 'L', 'S', 'H', 'K', 'Q', 'L', 'L', 'M', 'S', 'P', 'G', 'Q', 'S', 'T', 'S', 'T', 'T', 'F', 'P', 'A', 'D', 'A', 'P', 'A', 'G', 'E', 'Y', 'T', 'F', 'Y', 'C', 'E', 'P', 'H', 'R', 'G', 'A', 'G', 'M', 'V', 'G', 'K', 'I', 'T', 'V'], ['V', 'Q', 'I', 'K', 'M', 'G', 'T', 'D', 'K', 'Y', 'A', 'P', 'L', 'Y', 'E', 'P', 'K', 'A', 'L', 'S', 'I', 'S', 'A', 'G', 'D', 'T', 'V', 'E', 'F', 'V', 'M', 'N', 'K', 'V', 'G', 'P', 'H', 'N', 'V', 'I', 'F', 'D', 'K', '-', '-', 'V', 'P', 'A', 'G', '-', 'E', 'S', '-', 'A', 'P', 'A', 'L', 'S', 'N', 'T', 'K', 'L', 'R', 'I', 'A', 'P', 'G', 'S', 'F', 'Y', 'S', 'V', 'T', 'L', 'G', 'T', '-', '-', '-', 'P', 'G', 'T', 'Y', 'S', 'F', 'Y', 'C', 'T', 'P', 'H', 'R', 'G', 'A', 'G', 'M', 'V', 'G', 'T', 'I', 'T', 'V'], ['V', 'H', 'M', 'L', 'N', 'K', 'G', 'K', 'D', 'G', 'A', 'M', 'V', 'F', 'E', 'P', 'A', 'S', 'L', 'K', 'V', 'A', 'P', 'G', 'D', 'T', 'V', 'T', 'F', 'I', 'P', 'T', 'D', 'K', '-', 'G', 'H', 'N', 'V', 'E', 'T', 'I', 'K', 'G', 'M', 'I', 'P', 'D', 'G', '-', 'A', 'E', '-', 'A', '-', '-', '-', '-', '-', '-', '-', 'F', 'K', 'S', 'K', 'I', 'N', 'E', 'N', 'Y', 'K', 'V', 'T', 'F', 'T', 'A', '-', '-', '-', 'P', 'G', 'V', 'Y', 'G', 'V', 'K', 'C', 'T', 'P', 'H', 'Y', 'G', 'M', 'G', 'M', 'V', 'G', 'V', 'V', 'E', 'V']], dtype='U') # fmt: on ) ) self.assertEqual( repr(alignment), "" % id(alignment), ) self.assertEqual(len(alignment), 5) self.assertEqual(alignment.sequences[0].id, "plas_horvu") self.assertEqual(alignment.sequences[1].id, "plas_chlre") self.assertEqual(alignment.sequences[2].id, "plas_anava") self.assertEqual(alignment.sequences[3].id, "plas_proho") self.assertEqual(alignment.sequences[4].id, "azup_achcy") self.assertEqual( alignment.sequences[0].seq, "DVLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSGVDVSKISQEEYLTAPGETFSVTLTVPGTYGFYCEPHAGAGMVGKVTV", ) self.assertEqual( alignment.sequences[1].seq, "VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSGVNADAISRDDYLNAPGETYSVKLTAAGEYGYYCEPHQGAGMVGKIIV", ) self.assertEqual( alignment.sequences[2].seq, "VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKSADLAKSLSHKQLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKITV", ) self.assertEqual( alignment.sequences[3].seq, "VQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDKVPAGESAPALSNTKLRIAPGSFYSVTLGTPGTYSFYCTPHRGAGMVGTITV", ) self.assertEqual( alignment.sequences[4].seq, "VHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDKGHNVETIKGMIPDGAEAFKSKINENYKVTFTAPGVYGVKCTPHYGMGMVGVVEV", ) self.assertEqual( alignment.column_annotations["clustal_consensus"], " :: . : * :.: .*:*: * . **: * . . :*. . .. ...: . .* * * ** * **** : *", ) self.assertEqual( alignment[0], "D-VLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSG-VD-VSKISQEEYLTAPGETFSVTLTV---PGTYGFYCEPHAGAGMVGKVTV", ) self.assertEqual( alignment[1], "--VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSG-VN-ADAISRDDYLNAPGETYSVKLTA---AGEYGYYCEPHQGAGMVGKIIV", ) self.assertEqual( alignment[2], "--VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKSADLAKSLSHKQLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKITV", ) self.assertEqual( alignment[3], "VQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDK--VPAG-ES-APALSNTKLRIAPGSFYSVTLGT---PGTYSFYCTPHRGAGMVGTITV", ) self.assertEqual( alignment[4], "VHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDK-GHNVETIKGMIPDG-AE-A-------FKSKINENYKVTFTA---PGVYGVKCTPHYGMGMVGVVEV", ) self.assertEqual( str(alignment), """\ plas_horv 0 D-VLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSG-VD-VSKISQE plas_chlr 0 --VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSG-VN-ADAISRD plas_anav 0 --VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKSADLAKSLSHK plas_proh 0 VQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDK--VPAG-ES-APALSNT azup_achc 0 VHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDK-GHNVETIKGMIPDG-AE-A------ plas_horv 57 EYLTAPGETFSVTLTV---PGTYGFYCEPHAGAGMVGKVTV 95 plas_chlr 56 DYLNAPGETYSVKLTA---AGEYGYYCEPHQGAGMVGKIIV 94 plas_anav 58 QLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKITV 99 plas_proh 56 KLRIAPGSFYSVTLGT---PGTYSFYCTPHRGAGMVGTITV 94 azup_achc 51 -FKSKINENYKVTFTA---PGVYGVKCTPHYGMGMVGVVEV 88 """, ) self.assertEqual( format(alignment, "clustal"), """\ plas_horvu D-VLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSG- plas_chlre --VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSG- plas_anava --VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKS plas_proho VQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDK--VPAG- azup_achcy VHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDK-GHNVETIKGMIPDG- :: . : * :.: .*:*: * . **: * plas_horvu VD-VSKISQEEYLTAPGETFSVTLTV---PGTYGFYCEPHAGAGMVGKVT plas_chlre VN-ADAISRDDYLNAPGETYSVKLTA---AGEYGYYCEPHQGAGMVGKII plas_anava ADLAKSLSHKQLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKIT plas_proho ES-APALSNTKLRIAPGSFYSVTLGT---PGTYSFYCTPHRGAGMVGTIT azup_achcy AE-A-------FKSKINENYKVTFTA---PGVYGVKCTPHYGMGMVGVVE . . :*. . .. ...: . .* * * ** * **** : plas_horvu V plas_chlre V plas_anava V plas_proho V azup_achcy V * """, ) self.check_reading_writing(path) def test_empty(self): """Checking empty file.""" stream = StringIO() with self.assertRaises(ValueError): Align.parse(stream, "clustal") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)