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|
# 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),
"<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(
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),
"<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.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),
"<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.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),
"<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(
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),
"<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.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)
|
