mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:10:24 +08:00
74 lines
2.8 KiB
Python
74 lines
2.8 KiB
Python
#!/usr/bin/python
|
|
|
|
#
|
|
# 'remove_shorter_sequences.py'
|
|
#
|
|
# Script implemented to explore future functionalities of trimAl. The script
|
|
# analyzes the length of each sequence and remove those shorter than a given
|
|
# length set by the user
|
|
#
|
|
# [2015] S. Capella-Gutierrez - scapella@crg.es
|
|
#
|
|
# this script is free software: you can redistribute it and/or modify it under
|
|
# the terms of the GNU General Public License as published by the Free
|
|
# Software Foundation, the last available version.
|
|
#
|
|
# this script is distributed in the hope that it will be useful, but WITHOUT
|
|
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
|
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
|
|
# more details on <http://www.gnu.org/licenses/>
|
|
#
|
|
from Bio import AlignIO
|
|
import argparse
|
|
import sys
|
|
import os
|
|
|
|
if __name__ == "__main__":
|
|
|
|
parser = argparse.ArgumentParser()
|
|
|
|
parser.add_argument("-i", "--in", dest = "inFile", required = True, type = \
|
|
str, help = "Input alignment")
|
|
|
|
parser.add_argument("-o", "--out", dest = "outFile", default = None, type = \
|
|
str, help = "Set output file. It will be generated into FASTA format")
|
|
|
|
parser.add_argument("-m", "--min", dest = "minLen", default = 1, type = int,
|
|
help = "Set a minimum sequence length to keep it in the output alignment")
|
|
|
|
parser.add_argument("-f", "--format", dest = "inFormat", default = "fasta", \
|
|
type = str, choices = ["clustal", "fasta-m10", "fasta", "phylip-relaxed", \
|
|
"phylip-sequential", "phylip", "nexus"],help = "Set input alignment format")
|
|
|
|
parser.add_argument("-g", "--gap_symbol", dest = "gapSymbol", default = '-', \
|
|
type = str, help = "Define the gap symbol used in the input alignment")
|
|
|
|
parser.add_argument("--keep_header", dest = "keepHeader", default = False,
|
|
action = "store_true", help = "Keep original alignment sequence IDs indepen"
|
|
+ "dently of blank spaces on it")
|
|
|
|
parser.add_argument("-v", "--verbose", dest = "verbose", default = False,
|
|
action = "store_true", help = "Activate verbosity")
|
|
|
|
args = parser.parse_args()
|
|
|
|
if not os.path.isfile(args.inFile):
|
|
sys.exit(("ERROR: Check input alignment file '%s'") % (args.inFile))
|
|
|
|
ofile = open(args.outFile, "w") if args.outFile else sys.stdout
|
|
for record in AlignIO.read(args.inFile, format = args.inFormat):
|
|
sequence_id = record.id if not args.keepHeader else record.description
|
|
sequence = str(record.seq)
|
|
|
|
length = len(sequence)
|
|
valid = len([ps for ps in range(length) if sequence[ps] != args.gapSymbol])
|
|
|
|
if valid >= args.minLen:
|
|
print >> ofile, (">%s\n%s") % (sequence_id, sequence)
|
|
elif args.verbose:
|
|
msg = ("INFO: Sequence '%s' has been removed. Shorter ") % (sequence_id)
|
|
msg += ("(%d) than min. sequence length (%d)") % (valid, args.minLen)
|
|
print >> sys.stderr, msg
|
|
sys.stderr.flush()
|
|
ofile.close()
|