def test_kalign(self):
"""Make sure we can parse the Kalign header."""
path = "Clustalw/kalign.aln"
with open(path) as stream:
alignments = AlignmentIterator(stream)
self.assertEqual(alignments.program, "Kalign")
self.assertEqual(alignments.version, "2.0")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (2 rows x 27 columns) at 0x%x>" %
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.check_reading_writing(path)
def check_reading_writing(self, path):
alignments = AlignmentIterator(path)
stream = StringIO()
writer = AlignmentWriter(stream)
n = writer.write_file(alignments, mincount=1, maxcount=1)
self.assertEqual(n, 1)
alignments = AlignmentIterator(path)
alignment = next(alignments)
stream.seek(0)
saved_alignments = AlignmentIterator(stream)
self.assertEqual(saved_alignments.program, alignments.program)
self.assertEqual(saved_alignments.version, alignments.version)
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_muscle(self):
path = "Clustalw/muscle.aln"
# includes the sequence length on the right hand side of each line
with open(path) as stream:
alignments = AlignmentIterator(stream)
self.assertEqual(alignments.program, "MUSCLE")
self.assertEqual(alignments.version, "3.8")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (3 rows x 687 columns) at 0x%x>" %
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.check_reading_writing(path)
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 = AlignmentIterator(stream)
self.assertEqual(alignments.program, "CLUSTAL")
self.assertEqual(alignments.version, "1.81")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (2 rows x 601 columns) at 0x%x>" %
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.check_reading_writing(path)
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 = AlignmentIterator(stream)
self.assertEqual(alignments.program, "MSAPROBS")
self.assertEqual(alignments.version, "0.9.7")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (8 rows x 298 columns) at 0x%x>" %
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.check_reading_writing(path)
def test_empty(self):
"""Checking empty file."""
stream = StringIO()
with self.assertRaises(ValueError):
AlignmentIterator(stream)
def test_probcons(self):
path = "Clustalw/probcons.aln"
# example taken from the PROBCONS documentation
with open(path) as stream:
alignments = AlignmentIterator(stream)
self.assertEqual(alignments.program, "PROBCONS")
self.assertEqual(alignments.version, "1.12")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (5 rows x 101 columns) at 0x%x>" %
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.check_reading_writing(path)