/
ConcatenateFasta
executable file
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/
ConcatenateFasta
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fileencoding=utf-8
"""
TRANSLATE FASTA
James B. Pease
"""
import os
import sys
import argparse
from mixcore import fasta_iter
from random import randint
_LICENSE = """
http://www.github.org/jbpease/mixtape
MixTAPE: Mix of Tools for Analysis in Phylogenetics and Evolution
This file is part of MixTAPE.
MixTAPE 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, either version 3 of the License, or
(at your option) any later version.
MixTAPE 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.
You should have received a copy of the GNU General Public License
along with MixTAPE. If not, see <http://www.gnu.org/licenses/>.
"""
def generate_argparser():
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
epilog=_LICENSE)
parser.add_argument('fasta', nargs='*',
type=os.path.abspath,
help="input fasta file")
parser.add_argument("--search", help="original text to search for")
parser.add_argument("--replace",
help=("text to replace searched text"
"(leave blank to replace with nothing"))
parser.add_argument('--out', type=os.path.abspath,
required=True, help="output fasta file")
return parser
def main(arguments=None):
arguments = arguments if arguments is not None else sys.argv[1:]
parser = generate_argparser()
args = parser.parse_args(args=arguments)
randkey = randint(1e6,9e6)
for i, fastafile in enumerate(args.fasta):
if i == len(args.fasta) - 1:
with open(args.out, 'w') as outfile:
for hdr, seq in fasta_iter(fastafile):
other_sequences = open("{}-{}.tmp".format(
randkey, hdr)).read()
outfile.write(">{}\n{}{}\n".format(
hdr, other_sequences, seq))
else:
for hdr, seq in fasta_iter(fastafile):
with open("{}-{}.tmp".format(randkey, hdr), 'a') as outfile:
outfile.write(seq)
return ''
if __name__ == '__main__':
main()