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test_Align_a2m.py
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906 lines (865 loc) · 53.6 KB
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# Copyright 2006-2014 by Peter Cock. All rights reserved.
# Copyright 2022 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Bio.Align.a2m module."""
import unittest
from io import StringIO
import numpy as np
from Bio import Align
from Bio.Align import substitution_matrices
substitution_matrix = substitution_matrices.load("BLOSUM62")
class TestA2MReadingWriting(unittest.TestCase):
def check_reading_writing(self, path):
alignments = Align.parse(path, "a2m")
stream = StringIO()
n = Align.write(alignments, stream, "a2m")
self.assertEqual(n, 1)
alignments = Align.parse(path, "a2m")
alignment = next(alignments)
stream.seek(0)
saved_alignments = Align.parse(stream, "a2m")
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.a2m"
with open(path) as stream:
alignments = Align.parse(stream, "a2m")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.check_clustalw(alignment)
alignments = iter(alignments)
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.check_clustalw(alignment)
with Align.parse(path, "a2m") as alignments:
alignment = next(alignments)
self.check_clustalw(alignment)
with self.assertRaises(AttributeError):
alignments._stream
with Align.parse(path, "a2m") as alignments:
pass
with self.assertRaises(AttributeError):
alignments._stream
self.check_reading_writing(path)
def check_clustalw(self, alignment):
self.assertEqual(
repr(alignment),
"<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.assertEqual(
alignment.column_annotations["state"],
"DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDD",
)
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, "a2m"),
"""\
>gi|4959044|gb|AAD34209.1|AF069
MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNSESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSE.NSTCPICRRAVLSSGNRESVV
>gi|671626|emb|CAA85685.1|
---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPG-----------------VPPEEAGAAVAAESSTGT---------WTTVWTDGLTSLDRYKG-----RCYHIEPVPG-------------------EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAG-----------------------TCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVIPVASG-----------------------------GIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACVKARNEG---RDLAAEGNAIIREACKWSPElAAACEVWKEIKFEFPAMD---
""",
)
counts = alignment.counts(substitution_matrix)
self.assertEqual(
repr(counts),
"<AlignmentCounts object (substitution score = -34.0; 472 aligned letters; 64 identities; 408 mismatches; 126 positives; 129 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
substitution_score = -34.0,
aligned = 472:
identities = 64,
positives = 126,
mismatches = 408.
gaps = 129:
left_gaps = 9:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 9:
open_left_deletions = 1,
extend_left_deletions = 8;
internal_gaps = 117:
internal_insertions = 1:
open_internal_insertions = 1,
extend_internal_insertions = 0;
internal_deletions = 116:
open_internal_deletions = 8,
extend_internal_deletions = 108;
right_gaps = 3:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 3:
open_right_deletions = 1,
extend_right_deletions = 2.
""",
)
self.assertEqual(counts.left_insertions, 0)
self.assertEqual(counts.left_deletions, 9)
self.assertEqual(counts.right_insertions, 0)
self.assertEqual(counts.right_deletions, 3)
self.assertEqual(counts.internal_insertions, 1)
self.assertEqual(counts.internal_deletions, 116)
self.assertEqual(counts.left_gaps, 9)
self.assertEqual(counts.right_gaps, 3)
self.assertEqual(counts.internal_gaps, 117)
self.assertEqual(counts.insertions, 1)
self.assertEqual(counts.deletions, 128)
self.assertEqual(counts.gaps, 129)
self.assertEqual(counts.aligned, 472)
self.assertEqual(counts.identities, 64)
self.assertEqual(counts.mismatches, 408)
self.assertEqual(counts.positives, 126)
def test_msaprobs(self):
path = "Clustalw/msaprobs.a2m"
# This example was obtained from
# http://virgil.ruc.dk/kurser/Sekvens/Treedraw.htm
# and converted to A2M format.
with open(path) as stream:
alignments = Align.parse(stream, "a2m")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<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["state"],
"DDDDIIIIIIIIDDDIIIIDDDDDIDIIDDDDIIIIIIIIIIIIIIIIIIIDDDDDDDDDDDDDDDDDDDDDDDIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIIDDDDDDDDDDDDDDDDDDDDDDDIDDDDDDIDDDDDDDDDDDIIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIIII",
)
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, "a2m"),
"""\
>V_Harveyi_PATH
MKNW........IKV....AVAAI.A..LSAA...................TVQAATEVKVGMSGRYFPFTFVK..QDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRK.GNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT..GIEHDVALGRADAFIMDRLSALE.LIKKTG.LPLQLAGEPFE.....TIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK....
>B_subtilis_YXEM
MKMKkw......TVL....VVAALlA.vLSACgn............g.nssSKEDDNVLHVGATGQSYPFAYKE..NGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKK.DNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETqeGTLKDVAYGRVDAYVNSRTVLIA.QIKKTG.LPLKLAGDPIV.....YEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVeqkh
>FLIY_ECOLI
MKLAhlgrqalmGVM....AVALVaG..MSVKsf.........adeg.llnKVKERGTLLVGLEGTYPPFSFQGd.DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKgNEGTIKTADDLKGKKVGVGLGTNYEEWLRQN--VQGVDVRTYDDdpTKYQDLRVGRIDAILVDRLAALD.LVKKTN.DTLAVTGEAFS.....RQESGVALRK--GNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK....
>Deinococcus_radiodurans
MKKSll......SLKlsglLVPSVlAlsLSACss...............psSTLNQGTLKIAMEGTYPPFTSKNe.QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKnNTFNPQSLADLKGKRVGSTLGSNYEKQLI-D--TGDIKIVTYPGapEILADLVAGRIDAAYNDRLVVNY.IIND-QkLPVRGAGQIGD.....AAPVGIALKK--GNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQ...p
>B_subtilis_GlnH_homo_YCKK
MKKAll......ALF....MVVSIaA..LAACgagndnqskdnakdgdlwaSIKKKGVLTVGTEGTYEPFTYHDkdTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVGKTD-REDKYDFSDKYTTSRAVVVTKK.DNNDIKSEADVKGKTSAQSLTSNYNKLAT-N--A-GAKVEGVEGmaQALQMIQQARVDMTYNDKLAVLN.YLKTSGnKNVKIAFETGE.....PQSTYFTFRK--GSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK....
>YA80_HAEIN
MKKLlf......TTA....LLTGAiA..FSTFs...........hageiadRVEKTKTLLVGTEGTYAPFTFHDk.SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKS.SDNSIKSFEDLKGRKSAQSATSNWGKDAK-A--A-GAQILVVDGlaQSLELIKQGRAEATINDKLAVLD.YFKQHPnSGLKIAYDRGD.....KTPTAFAFLQ--GEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ....
>E_coli_GlnH
MKSVl.......KVS....LAALTlA..FAVSsh.........a.......---ADKKLVVATDTAFVPFEFKQ..GDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKAn-NNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNidNAYMELGTNRADAVLHDTPNILY.FIKTAGnGQFKAVGDSLE.....AQQYGIAFPK--GSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP-K....
>HISJ_E_COLI
MKKLvl......SLS....LV---lA..FSSAta...............a.FAAIPQNIRIGTDPTYAPFESKNs.QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK.NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGqdNIYSDLTAGRIDAAFQDEVAASEgFLKQPVgKDYKFGGPSVKdeklfGVGTGMGLRK--EDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYG...g
""",
)
counts = alignment.counts(substitution_matrix)
self.assertEqual(
repr(counts),
"<AlignmentCounts object (substitution score = 10664.0; 6948 aligned letters; 2353 identities; 4595 mismatches; 3745 positives; 608 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
substitution_score = 10664.0,
aligned = 6948:
identities = 2353,
positives = 3745,
mismatches = 4595.
gaps = 608:
left_gaps = 0:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 0:
open_left_deletions = 0,
extend_left_deletions = 0;
internal_gaps = 578:
internal_insertions = 285:
open_internal_insertions = 126,
extend_internal_insertions = 159;
internal_deletions = 293:
open_internal_deletions = 125,
extend_internal_deletions = 168;
right_gaps = 30:
right_insertions = 11:
open_right_insertions = 8,
extend_right_insertions = 3;
right_deletions = 19:
open_right_deletions = 7,
extend_right_deletions = 12.
""",
)
self.assertEqual(counts.left_insertions, 0)
self.assertEqual(counts.left_deletions, 0)
self.assertEqual(counts.right_insertions, 11)
self.assertEqual(counts.right_deletions, 19)
self.assertEqual(counts.internal_insertions, 285)
self.assertEqual(counts.internal_deletions, 293)
self.assertEqual(counts.left_gaps, 0)
self.assertEqual(counts.right_gaps, 30)
self.assertEqual(counts.internal_gaps, 578)
self.assertEqual(counts.insertions, 296)
self.assertEqual(counts.deletions, 312)
self.assertEqual(counts.gaps, 608)
self.assertEqual(counts.aligned, 6948)
self.assertEqual(counts.identities, 2353)
self.assertEqual(counts.mismatches, 4595)
self.assertEqual(counts.positives, 3745)
self.check_reading_writing(path)
def test_muscle(self):
path = "Clustalw/muscle.a2m"
with open(path) as stream:
alignments = Align.parse(stream, "a2m")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<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["state"],
"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDI",
)
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, "a2m"),
"""\
>Test1seq
.................................................................AGTTACAATAACTGACGAAGCTAAGTAGGCTACTAATTAACGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGTAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATCGTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACAAAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAACGTAAACAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTTCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACGGTCGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTT.
>AT3G20900.1-SEQ
atgaacaaagtagcgaggaagaacaaaacatcaggtgaacaaaaaaaaaactcaatccacatcaaAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAAATTAAAGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGCAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATAGTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAACAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTAATACTACTTTCTGTATTGATCCTATATCAAAAAAAAAAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTGCGTTGACGAAGAAGAGCTCTATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAg
>AT3G20900.1-CDS
.................................................................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGAACAAAGTAGCGAGGAAGAA------------------------------CAAAACATC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCCGGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAg
""",
)
counts = alignment.counts()
self.assertEqual(
repr(counts),
"<AlignmentCounts object (1034 aligned letters; 974 identities; 60 mismatches; 962 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
aligned = 1034:
identities = 974,
mismatches = 60.
gaps = 962:
left_gaps = 556:
left_insertions = 65:
open_left_insertions = 1,
extend_left_insertions = 64;
left_deletions = 491:
open_left_deletions = 2,
extend_left_deletions = 489;
internal_gaps = 404:
internal_insertions = 0:
open_internal_insertions = 0,
extend_internal_insertions = 0;
internal_deletions = 404:
open_internal_deletions = 4,
extend_internal_deletions = 400;
right_gaps = 2:
right_insertions = 2:
open_right_insertions = 2,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
self.assertEqual(counts.left_insertions, 65)
self.assertEqual(counts.left_deletions, 491)
self.assertEqual(counts.right_insertions, 2)
self.assertEqual(counts.right_deletions, 0)
self.assertEqual(counts.internal_insertions, 0)
self.assertEqual(counts.internal_deletions, 404)
self.assertEqual(counts.left_gaps, 556)
self.assertEqual(counts.right_gaps, 2)
self.assertEqual(counts.internal_gaps, 404)
self.assertEqual(counts.insertions, 67)
self.assertEqual(counts.deletions, 895)
self.assertEqual(counts.gaps, 962)
self.assertEqual(counts.aligned, 1034)
self.assertEqual(counts.identities, 974)
self.assertEqual(counts.mismatches, 60)
self.check_reading_writing(path)
def test_kalign(self):
path = "Clustalw/kalign.a2m"
with open(path) as stream:
alignments = Align.parse(stream, "a2m")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<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.assertEqual(
alignment.column_annotations["state"],
"DDDDDDDDDDDDDDDDDDDDDDDDDID",
)
self.assertEqual(
str(alignment),
"""\
Test1seq 0 GCTGGGGATGGAGAGGGAACAGAGT-T 26
0 |||||||||||||||||||||||||-. 27
AT3G20900 0 GCTGGGGATGGAGAGGGAACAGAGTAG 27
""",
)
self.assertEqual(
format(alignment, "a2m"),
"""\
>Test1seq
GCTGGGGATGGAGAGGGAACAGAGT.T
>AT3G20900
GCTGGGGATGGAGAGGGAACAGAGTaG
""",
)
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
)
)
counts = alignment.counts()
self.assertEqual(
repr(counts),
"<AlignmentCounts object (26 aligned letters; 25 identities; 1 mismatches; 1 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
aligned = 26:
identities = 25,
mismatches = 1.
gaps = 1:
left_gaps = 0:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 0:
open_left_deletions = 0,
extend_left_deletions = 0;
internal_gaps = 1:
internal_insertions = 1:
open_internal_insertions = 1,
extend_internal_insertions = 0;
internal_deletions = 0:
open_internal_deletions = 0,
extend_internal_deletions = 0;
right_gaps = 0:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
self.assertEqual(counts.left_insertions, 0)
self.assertEqual(counts.left_deletions, 0)
self.assertEqual(counts.right_insertions, 0)
self.assertEqual(counts.right_deletions, 0)
self.assertEqual(counts.internal_insertions, 1)
self.assertEqual(counts.internal_deletions, 0)
self.assertEqual(counts.left_gaps, 0)
self.assertEqual(counts.right_gaps, 0)
self.assertEqual(counts.internal_gaps, 1)
self.assertEqual(counts.insertions, 1)
self.assertEqual(counts.deletions, 0)
self.assertEqual(counts.gaps, 1)
self.assertEqual(counts.aligned, 26)
self.assertEqual(counts.identities, 25)
self.assertEqual(counts.mismatches, 1)
self.check_reading_writing(path)
def test_probcons(self):
path = "Clustalw/probcons.a2m"
# example taken from the PROBCONS documentation,
# and converted to aligned A2M format.
with open(path) as stream:
alignments = Align.parse(stream, "a2m")
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<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[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(
alignment.column_annotations["state"],
"DIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIDDIDDDDDDDDDDDDDDDDDDDDDDDIIIDDDDDDDDDDDDDDDDDDDDDD",
)
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, "a2m"),
"""\
>plas_horvu
D.VLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSG.VD.VSKISQEEYLTAPGETFSVTLTV...PGTYGFYCEPHAGAGMVGKVTV
>plas_chlre
-.VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSG.VN.ADAISRDDYLNAPGETYSVKLTA...AGEYGYYCEPHQGAGMVGKIIV
>plas_anava
-.VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKsADlAKSLSHKQLLMSPGQSTSTTFPAdapAGEYTFYCEPHRGAGMVGKITV
>plas_proho
VqIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDK--VPAG.ES.APALSNTKLRIAPGSFYSVTLGT...PGTYSFYCTPHRGAGMVGTITV
>azup_achcy
VhMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDK-GHNVETIKGMIPDG.AE.A-------FKSKINENYKVTFTA...PGVYGVKCTPHYGMGMVGVVEV
""",
)
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
)
)
counts = alignment.counts(substitution_matrix)
self.assertEqual(
repr(counts),
"<AlignmentCounts object (substitution score = 2197.0; 904 aligned letters; 427 identities; 477 mismatches; 554 positives; 72 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
substitution_score = 2197.0,
aligned = 904:
identities = 427,
positives = 554,
mismatches = 477.
gaps = 72:
left_gaps = 10:
left_insertions = 8:
open_left_insertions = 4,
extend_left_insertions = 4;
left_deletions = 2:
open_left_deletions = 2,
extend_left_deletions = 0;
internal_gaps = 62:
internal_insertions = 14:
open_internal_insertions = 9,
extend_internal_insertions = 5;
internal_deletions = 48:
open_internal_deletions = 17,
extend_internal_deletions = 31;
right_gaps = 0:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
self.assertEqual(counts.left_insertions, 8)
self.assertEqual(counts.left_deletions, 2)
self.assertEqual(counts.right_insertions, 0)
self.assertEqual(counts.right_deletions, 0)
self.assertEqual(counts.internal_insertions, 14)
self.assertEqual(counts.internal_deletions, 48)
self.assertEqual(counts.left_gaps, 10)
self.assertEqual(counts.right_gaps, 0)
self.assertEqual(counts.internal_gaps, 62)
self.assertEqual(counts.insertions, 22)
self.assertEqual(counts.deletions, 50)
self.assertEqual(counts.gaps, 72)
self.assertEqual(counts.aligned, 904)
self.assertEqual(counts.identities, 427)
self.assertEqual(counts.mismatches, 477)
self.assertEqual(counts.positives, 554)
self.check_reading_writing(path)
def test_empty(self):
"""Checking empty file."""
stream = StringIO()
alignments = Align.parse(stream, "a2m")
with self.assertRaises(ValueError) as cm:
next(alignments)
self.assertEqual(str(cm.exception), "Empty file.")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)