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Bio.Align parser/writer for A2M alignment files (#3966)
* test files * test script * add module * add state column annotation * update
This commit is contained in:
mdehoon
GitHub
130
Bio/Align/a2m.py
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130
Bio/Align/a2m.py
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@ -0,0 +1,130 @@
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# Copyright 2022 by Michiel de Hoon. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Bio.Align support for A2M files.
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A2M files are alignment files created by align2model or hmmscore in the SAM
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Sequence Alignment and Modeling Software System.
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"""
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from Bio.Align import Alignment
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from Bio.Align import interfaces
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from Bio.Seq import Seq
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from Bio.SeqRecord import SeqRecord
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from Bio import BiopythonExperimentalWarning
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import warnings
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warnings.warn(
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"Bio.Align.a2m is an experimental module which may undergo "
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"significant changes prior to its future official release.",
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BiopythonExperimentalWarning,
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)
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class AlignmentWriter(interfaces.AlignmentWriter):
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"""Alignment file writer for the A2M file format."""
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def __init__(self, target):
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"""Create an AlignmentWriter object.
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Arguments:
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- target - output stream or file name
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"""
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super().__init__(target, mode="w")
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def format_alignment(self, alignment):
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"""Return a string with the alignment in the A2M file format."""
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if not isinstance(alignment, Alignment):
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raise TypeError("Expected an Alignment object")
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lines = []
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state = alignment.column_annotations["state"]
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for sequence, line in zip(alignment.sequences, alignment):
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lines.append(f">{sequence.id} {sequence.description}")
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s = ""
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for c, m in zip(line, state):
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if m == "D":
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s += c.upper()
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elif m == "I":
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if c == "-":
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s += "."
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else:
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s += c.lower()
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lines.append(s)
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return "\n".join(lines)
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class AlignmentIterator(interfaces.AlignmentIterator):
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"""Alignment iterator for files in the A2M file format.
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An A2M file contains one multiple alignment. Matches are represented by
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upper case letters and deletions by dashes in alignment columns containing
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matches or deletions only. Insertions are represented by lower case letters,
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with gaps aligned to the insertion shown as periods. Header lines start
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with '>' followed by the name of the sequence, and optionally a description.
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"""
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def __init__(self, source):
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"""Create an AlignmentIterator object.
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Arguments:
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- source - input data or file name
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"""
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super().__init__(source, mode="t", fmt="A2M")
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def parse(self, stream):
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"""Parse the next alignment from the stream."""
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names = []
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descriptions = []
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lines = []
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for line in stream:
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if line.startswith(">"):
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parts = line[1:].rstrip().split(None, 1)
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try:
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name, description = parts
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except ValueError:
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name = parts[0]
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description = None
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names.append(name)
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descriptions.append(description)
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lines.append("")
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else:
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lines[-1] += line.strip()
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if not lines:
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raise ValueError("Empty file.")
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state = ""
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for c in lines[0]:
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if c == "-" or c.isupper():
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state += "D" # Match/deletion state
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elif c == "." or c.islower():
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state += "I" # Insertion state
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else:
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raise Exception("Unexpected letter '%s' in alignment" % c)
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for line in lines[1:]:
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for c, m in zip(line, state):
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if m == "D": # Match/deletion state
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assert c == "-" or c.isupper()
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elif m == "I": # Insertion state
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assert c == "." or c.islower()
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else:
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raise Exception("Unexpected letter '%s' in alignment" % c)
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for i, line in enumerate(lines):
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lines[i] = line.upper().replace(".", "-")
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coordinates = Alignment.infer_coordinates(lines)
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records = []
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for name, description, line in zip(names, descriptions, lines):
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line = line.replace("-", "")
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sequence = Seq(line)
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if description is None:
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record = SeqRecord(sequence, name)
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else:
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record = SeqRecord(sequence, name, description=description)
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records.append(record)
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alignment = Alignment(records, coordinates)
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alignment.column_annotations = {}
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alignment.column_annotations["state"] = state
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yield alignment
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16
Tests/Clustalw/clustalw.a2m
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16
Tests/Clustalw/clustalw.a2m
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>gi|4959044|gb|AAD34209.1|AF069
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MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW
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LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE
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VPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS
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ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLR
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QIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESG
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SLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSE.NSTCPICRRAVLSSGNRESV
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V
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>gi|671626|emb|CAA85685.1|
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---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPG-----------------VPPEEAGAAVAAESSTGT---------
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WTTVWTDGLTSLDRYKG-----RCYHIEPVPG-------------------EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP
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VAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN
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ATAG-----------------------TCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKAL
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RLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVIPVASG-----------------------------GIHVWHMPA
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LTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACVKARNEG---RDLAAEGNAIIREACKWSPElAAACEVWKEIKFEFPAMD--
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-
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4
Tests/Clustalw/kalign.a2m
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4
Tests/Clustalw/kalign.a2m
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>Test1seq
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GCTGGGGATGGAGAGGGAACAGAGT.T
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>AT3G20900
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GCTGGGGATGGAGAGGGAACAGAGTaG
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32
Tests/Clustalw/msaprobs.a2m
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32
Tests/Clustalw/msaprobs.a2m
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>V_Harveyi_PATH
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MKNW........IKV....AVAAI.A..LSAA...................TVQAATEVKVGMSGRYFPFTFVK..QDKLQGFEVDMWDEIGKRNDYKIE
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YVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRK.GNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT..G
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IEHDVALGRADAFIMDRLSALE.LIKKTG.LPLQLAGEPFE.....TIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK....
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>B_subtilis_YXEM
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MKMKkw......TVL....VVAALlA.vLSACgn............g.nssSKEDDNVLHVGATGQSYPFAYKE..NGKLTGFDVEVMEAVAKKIDMKLD
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WKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKK.DNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETqeG
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TLKDVAYGRVDAYVNSRTVLIA.QIKKTG.LPLKLAGDPIV.....YEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVeqkh
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>FLIY_ECOLI
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MKLAhlgrqalmGVM....AVALVaG..MSVKsf.........adeg.llnKVKERGTLLVGLEGTYPPFSFQGd.DGKLTGFEVEFAQQLAKHLGVEAS
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LKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKgNEGTIKTADDLKGKKVGVGLGTNYEEWLRQN--VQGVDVRTYDDdpT
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KYQDLRVGRIDAILVDRLAALD.LVKKTN.DTLAVTGEAFS.....RQESGVALRK--GNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK....
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>Deinococcus_radiodurans
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MKKSll......SLKlsglLVPSVlAlsLSACss...............psSTLNQGTLKIAMEGTYPPFTSKNe.QGELVGFDVDIAKAVAQKLNLKPE
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FVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKnNTFNPQSLADLKGKRVGSTLGSNYEKQLI-D--TGDIKIVTYPGapE
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ILADLVAGRIDAAYNDRLVVNY.IIND-QkLPVRGAGQIGD.....AAPVGIALKK--GNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQ...p
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>B_subtilis_GlnH_homo_YCKK
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MKKAll......ALF....MVVSIaA..LAACgagndnqskdnakdgdlwaSIKKKGVLTVGTEGTYEPFTYHDkdTDKLTGYDVEVITEVAKRLGLKVD
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FKETQWGSMFAGLNSKRFDVVANQVGKTD-REDKYDFSDKYTTSRAVVVTKK.DNNDIKSEADVKGKTSAQSLTSNYNKLAT-N--A-GAKVEGVEGmaQ
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ALQMIQQARVDMTYNDKLAVLN.YLKTSGnKNVKIAFETGE.....PQSTYFTFRK--GSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK....
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>YA80_HAEIN
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MKKLlf......TTA....LLTGAiA..FSTFs...........hageiadRVEKTKTLLVGTEGTYAPFTFHDk.SGKLTGFDVEVIRKVAEKLGLKVE
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FKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKS.SDNSIKSFEDLKGRKSAQSATSNWGKDAK-A--A-GAQILVVDGlaQ
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SLELIKQGRAEATINDKLAVLD.YFKQHPnSGLKIAYDRGD.....KTPTAFAFLQ--GEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ....
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>E_coli_GlnH
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MKSVl.......KVS....LAALTlA..FAVSsh.........a.......---ADKKLVVATDTAFVPFEFKQ..GDKYVGFDVDLWAAIAKELKLDYE
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LKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKAn-NNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNidN
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AYMELGTNRADAVLHDTPNILY.FIKTAGnGQFKAVGDSLE.....AQQYGIAFPK--GSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP-K....
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>HISJ_E_COLI
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MKKLvl......SLS....LV---lA..FSSAta...............a.FAAIPQNIRIGTDPTYAPFESKNs.QGELVGFDIDLAKELCKRINTQCT
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FVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK.NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGqdN
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IYSDLTAGRIDAAFQDEVAASEgFLKQPVgKDYKFGGPSVKdeklfGVGTGMGLRK--EDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYG...g
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24
Tests/Clustalw/muscle.a2m
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24
Tests/Clustalw/muscle.a2m
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@ -0,0 +1,24 @@
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>Test1seq
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.................................................................AGTTACAATAACTGACGAAGCTAAGTAGGCTACTA
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ATTAACGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGTAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATC
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GTATTCCGGTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAATAAATTAGCGCCAAAATAATGAAAAAAATAATAACAAACA
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AAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGCTGAATTTTGATCACCTGCTA
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ATACTACTTTCTGTATTGATCCTATATCAACGTAAACAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTTCGTTGACGAAGAAGAGCTC
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TATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACGGTCGCTAGAGAAACTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC
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GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCGTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTT.
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>AT3G20900.1-SEQ
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atgaacaaagtagcgaggaagaacaaaacatcaggtgaacaaaaaaaaaactcaatccacatcaaAGTTACAATAACTGACGAAGCTAAGTAGGCTAGAA
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ATTAAAGTCATCAACCTAATACATAGCACTTAGAAAAAAGTGAAGCAAGAAAATATAAAATAATAAAAGGGTGGGTTATCAATTGATAGTGTAAATCATA
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GTTGATTTTTGATATACCCTACCACAAAAACTCAAACCGACTTGATTCAAATCATCTCAAAAAACAAGCGCCAAAATAATGAAAAAAATAATAACAAAAA
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CAAACAAACCAAAATAAGAAAAAACATTACGCAAAACATAATAATTTACTCTTCGTTATTGTATTAACAAATCAAAGAGATGAATTTTGATCACCTGCTA
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ATACTACTTTCTGTATTGATCCTATATCAAAAAAAAAAAAGATACTAATAATTAACTAAAAGTACGTTCATCGATCGTGTGCGTTGACGAAGAAGAGCTC
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TATCTCCGGCGGAGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC
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GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAg
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>AT3G20900.1-CDS
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.................................................................-----------------------------------
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----------------------------------------------------------------------------------------------------
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------------------------------------------------------------------------------ATGAACAAAGTAGCGAGGAAGA
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A------------------------------CAAAACATC------------------------------------------------------------
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----------------------------------------------------------------------------------------------------
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------------AGCAAAGAAAACGATCTGTCTCCGTCGTAACACACAGTTTTTCGAGACCCTTTGCTTCTTCGGCGCCGGTGGACACGTCAGCATCTCC
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GGTATCCTAGACTTCTTGGCTTTCGGGGTACAACAACCGCCTGGTGACGTCAGCACCGCTGCTGGGGATGGAGAGGGAACAGAGTAg
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15
Tests/Clustalw/probcons.a2m
Normal file
15
Tests/Clustalw/probcons.a2m
Normal file
@ -0,0 +1,15 @@
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>plas_horvu
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D.VLLGANGGVLVFEPNDFSVKAGETITFKNNAGYPHNVVFDEDAVPSG.VD.VSKISQEEYLTAPGETFSVTLTV...PGTYGFYCEPHAGAGMVGKVT
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V
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>plas_chlre
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-.VKLGADSGALEFVPKTLTIKSGETVNFVNNAGFPHNIVFDEDAIPSG.VN.ADAISRDDYLNAPGETYSVKLTA...AGEYGYYCEPHQGAGMVGKII
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V
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>plas_anava
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-.VKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKsADlAKSLSHKQLLMSPGQSTSTTFPAdapAGEYTFYCEPHRGAGMVGKIT
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V
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>plas_proho
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VqIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDK--VPAG.ES.APALSNTKLRIAPGSFYSVTLGT...PGTYSFYCTPHRGAGMVGTIT
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V
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>azup_achcy
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VhMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDK-GHNVETIKGMIPDG.AE.A-------FKSKINENYKVTFTA...PGVYGVKCTPHYGMGMVGVVE
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V
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321
Tests/test_Align_a2m.py
Normal file
321
Tests/test_Align_a2m.py
Normal file
@ -0,0 +1,321 @@
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# Copyright 2006-2014 by Peter Cock. All rights reserved.
|
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# 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."""
|
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import unittest
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import warnings
|
||||
|
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from io import StringIO
|
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from Bio import BiopythonExperimentalWarning
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", BiopythonExperimentalWarning)
|
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from Bio.Align.a2m import AlignmentIterator
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from Bio.Align.a2m import AlignmentWriter
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class TestA2MReadingWriting(unittest.TestCase):
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def check_reading_writing(self, path):
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alignments = AlignmentIterator(path)
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stream = StringIO()
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writer = AlignmentWriter(stream)
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n = writer.write_file(alignments, mincount=1, maxcount=1)
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self.assertEqual(n, 1)
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alignments = AlignmentIterator(path)
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alignment = next(alignments)
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stream.seek(0)
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saved_alignments = AlignmentIterator(stream)
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saved_alignment = next(saved_alignments)
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with self.assertRaises(StopIteration):
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next(saved_alignments)
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self.assertEqual(len(alignment), len(saved_alignment))
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for i, (sequence, saved_sequence) in enumerate(
|
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zip(alignment.sequences, saved_alignment.sequences)
|
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):
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self.assertEqual(sequence.id, saved_sequence.id)
|
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self.assertEqual(sequence.seq, saved_sequence.seq)
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self.assertEqual(alignment[i], saved_alignment[i])
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|
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def test_clustalw(self):
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path = "Clustalw/clustalw.a2m"
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with open(path) as stream:
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alignments = AlignmentIterator(stream)
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alignment = next(alignments)
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with self.assertRaises(StopIteration):
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next(alignments)
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self.assertEqual(
|
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repr(alignment),
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"<Bio.Align.Alignment object (2 rows x 601 columns) at 0x%x>"
|
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% id(alignment),
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)
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self.assertEqual(len(alignment), 2)
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self.assertEqual(alignment.sequences[0].id, "gi|4959044|gb|AAD34209.1|AF069")
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self.assertEqual(alignment.sequences[1].id, "gi|671626|emb|CAA85685.1|")
|
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self.assertEqual(
|
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alignment.sequences[0].seq,
|
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"MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNSESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGSSSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV",
|
||||
)
|
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self.assertEqual(
|
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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.check_reading_writing(path)
|
||||
|
||||
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 = AlignmentIterator(stream)
|
||||
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["state"],
|
||||
"DDDDIIIIIIIIDDDIIIIDDDDDIDIIDDDDIIIIIIIIIIIIIIIIIIIDDDDDDDDDDDDDDDDDDDDDDDIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIIDDDDDDDDDDDDDDDDDDDDDDDIDDDDDDIDDDDDDDDDDDIIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDIIII",
|
||||
)
|
||||
self.check_reading_writing(path)
|
||||
|
||||
def test_muscle(self):
|
||||
path = "Clustalw/muscle.a2m"
|
||||
with open(path) as stream:
|
||||
alignments = AlignmentIterator(stream)
|
||||
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["state"],
|
||||
"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDI",
|
||||
)
|
||||
self.check_reading_writing(path)
|
||||
|
||||
def test_kalign(self):
|
||||
path = "Clustalw/kalign.a2m"
|
||||
with open(path) as stream:
|
||||
alignments = AlignmentIterator(stream)
|
||||
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.assertEqual(
|
||||
alignment.column_annotations["state"],
|
||||
"DDDDDDDDDDDDDDDDDDDDDDDDDID",
|
||||
)
|
||||
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 = AlignmentIterator(stream)
|
||||
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[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.check_reading_writing(path)
|
||||
|
||||
def test_empty(self):
|
||||
"""Checking empty file."""
|
||||
stream = StringIO()
|
||||
alignments = AlignmentIterator(stream)
|
||||
with self.assertRaises(ValueError):
|
||||
next(alignments)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
runner = unittest.TextTestRunner(verbosity=2)
|
||||
unittest.main(testRunner=runner)
|
||||
Reference in New Issue
Block a user