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108 lines
4.1 KiB
Python
108 lines
4.1 KiB
Python
#!/usr/bin/python
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#
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# 'check_codon_alignments.py'
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#
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# Script implemented to analyze resulting back-translated alignments by trimAl
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# Main idea here is to remove those codon-columns composed by only 'N'/'n' -
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# which are the symbol to indicate indeterminate nucleotides.
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#
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# [2014] S. Capella-Gutierrez - scapella@crg.es
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#
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# this script is free software: you can redistribute it and/or modify it under
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# the terms of the GNU General Public License as published by the Free
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# Software Foundation, the last available version.
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#
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# this script is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
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# more details on <http://www.gnu.org/licenses/>
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#
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from Bio import AlignIO
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import numpy as np
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import argparse
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import sys
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import os
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def splitSequence(seq, length = 80):
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''' Split a given sequence contained in one line into lines of size "length"
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'''
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return "\n".join([seq[i:i + length] for i in range(0, len(seq), length)])
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if __name__ == "__main__":
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parser = argparse.ArgumentParser()
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parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
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str, help = "Input alignment")
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parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
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str, help = "Set output file")
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parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
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type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
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"phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
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parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
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type = str, help = "Set the gap symbol used in the input alignment")
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parser.add_argument("--indeter_symbol", dest = "indeterSymbol", default = 'N',
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type = str, help = "Set the indetermination symbol used in the alignment")
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parser.add_argument("--keep_header", dest = "keepHeader", default = False,
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action = "store_true", help = "Keep original alignment sequence IDs indepen"
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+ "dently of blank spaces on it")
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parser.add_argument("--complementary", dest = "complement", default = False,
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action = "store_true", help = "Get the complementary output alignment")
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parser.add_argument("-v", "--verbose", dest = "verbose", default = False,
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action = "store_true", help = "Activate verbosity")
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args = parser.parse_args()
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if not os.path.isfile(args.inFile):
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sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
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alignment, alignment_length = {}, 0
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for record in AlignIO.read(args.inFile, format = args.inFormat):
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sequence_id = record.id if not args.keepHeader else record.description
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alignment.setdefault(sequence_id, str(record.seq))
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## Check all sequences have the same length
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if alignment_length == 0:
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alignment_length = len(str(record.seq))
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if alignment_length != len(str(record.seq)):
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sys.exit("ERROR: Check input alignment. Sequences with different lengths")
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## Check input alignment is multiple of 3
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if (alignment_length % 3) != 0:
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sys.exit("ERROR: Check input alignment. Its length is not multiple of 3")
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indetermination_cols = []
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indet = set([args.indeterSymbol.upper()])
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for pos in range(0, alignment_length, 3):
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onlyIndeter = True
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for col in range(pos, pos+3):
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column = set([alignment[seq][col].upper() for seq in alignment \
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if alignment[seq][col] != args.gapSymbol])
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if column ^ indet != set():
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onlyIndeter = False
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if onlyIndeter and not args.complement:
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indetermination_cols.append(pos)
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elif not onlyIndeter and args.complement:
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indetermination_cols.append(pos)
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if args.verbose and indetermination_cols:
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output = ",".join(map(str, sorted(indetermination_cols)))
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print >> sys.stderr, ("%s\t%s") % (args.inFile, output)
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ofile = open(args.outFile, "w") if args.outFile else sys.stdout
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for seq_id in alignment:
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output = "".join([alignment[seq_id][pos:pos+3] for pos in \
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range(0, alignment_length, 3) if not pos in indetermination_cols])
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print >> ofile, (">%s\n%s") % (seq_id, splitSequence(output))
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ofile.close()
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