fasta-get-faa.py

#! /usr/bin/env python


"""
extract sequences from FASTA file according to names in provided file
ignores text in the names file after the first tab
this version is modified to ignore anything after the underscore ("_") in the fasta header
usage:
python fasta-get-faa.py file.faa names.txt

Copyright:

    fasta-get-faa.py Extract FASTA sequences based on entry headers
    Copyright (C) 2022  William Brazelton

    This program 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.

    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
"""

import sys
fastafilename = sys.argv[1]
namesfilename = sys.argv[2]
outfilename = fastafilename + '.select.fa'

l = []
with open(namesfilename) as namesfile:
	for name in namesfile: 
		name = name.split('\t')
		name = name[0]
		l.append(name.strip('\n'))

from Bio import SeqIO

with open(outfilename,'a') as outfile:
	for fasta in SeqIO.parse(fastafilename,'fasta'):
		header = fasta.id
		header = header.split("_")
		header = 'c_' + header[1]
		print(header)
		if header in l: SeqIO.write(fasta,outfile,'fasta')