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74 lines
2.8 KiB
Python
74 lines
2.8 KiB
Python
#!/usr/bin/python
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#
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# 'remove_shorter_sequences.py'
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#
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# Script implemented to explore future functionalities of trimAl. The script
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# analyzes the length of each sequence and remove those shorter than a given
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# length set by the user
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#
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# [2015] 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 argparse
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import sys
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import os
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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. It will be generated into FASTA format")
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parser.add_argument("-m", "--min", dest = "minLen", default = 1, type = int,
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help = "Set a minimum sequence length to keep it in the output alignment")
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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 = "Define the gap symbol used in the input 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("-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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ofile = open(args.outFile, "w") if args.outFile else sys.stdout
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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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sequence = str(record.seq)
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length = len(sequence)
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valid = len([ps for ps in range(length) if sequence[ps] != args.gapSymbol])
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if valid >= args.minLen:
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print >> ofile, (">%s\n%s") % (sequence_id, sequence)
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elif args.verbose:
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msg = ("INFO: Sequence '%s' has been removed. Shorter ") % (sequence_id)
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msg += ("(%d) than min. sequence length (%d)") % (valid, args.minLen)
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print >> sys.stderr, msg
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sys.stderr.flush()
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ofile.close()
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