remove_fastas.py

#!/usr/bin/env python
###############################################
# Author: B. Anderson
# Date: 28 Jun 2019
# Updated: Oct 2021 (can now take a text file with strings for string matching, one per line; also cleaned up and added parser)
# Updated: Jun 2022; Mar 2026 (added quiet argument; adjusted for improved speed with many files)
# Description: a script to simply remove entries from multifastas based on string matches (arg1)
###############################################


import sys
import os
import argparse
from Bio import SeqIO


# instantiate the parser
parser = argparse.ArgumentParser(description = 'A script to remove fasta entries based on string matching. ' +
	'The new fasta files are output in the current directory with prefix \"mod_\".')


# add arguments to parse
parser.add_argument('strings', type = str, help = 'The comma delimited strings to search for ' +
	'when removing fastas from the multifastas (or nothing if file specified), ' +
	'and then the space-delimited multifastas', nargs = '*')
parser.add_argument('-f', type = str, dest = 'string_file', help = 'A text file with a list of strings, ' +
	'one per line (optional). If not specified, then the first space-delimited command line argument ' +
	'will be interpreted as the comma-delimited search strings.')
parser.add_argument('--quiet', '-q', action = 'store_true', help = 'Whether to silence screen reporting [default do not]')


# parse the command line
if len(sys.argv[1:]) == 0:		# if there are no arguments
	parser.print_help(sys.stderr)
	sys.exit(1)

args = parser.parse_args()

strings = args.strings
string_file = args.string_file

if not strings:
	parser.print_help(sys.stderr)
	sys.exit(1)

string_list = []
file_list = []
if not string_file:			# if there is no file specified with '-f'
	search_strings = strings[0]
	for part in search_strings.split(','):
		string_list.append(part)
	for fasta in strings[1:]:
		file_list.append(fasta)
else:
	with open(string_file, 'r') as str_file:
		for line in str_file:
			string_list.append(line.rstrip())
	for fasta in strings:
		file_list.append(fasta)


# read in the each multifasta file and remove entries
# Now updated to instead selectively store rather than remove
master_list = []
for multifasta in file_list:
	filename = os.path.basename(multifasta)
	fasta_list = []
	removed = 0
	fastas = SeqIO.parse(open(multifasta, 'r'), 'fasta')
	for fasta in fastas:
		store = True
		for string in string_list:
			if string in fasta.description:
				store = False
				removed = removed + 1
				break

		if store:
			fasta_list.append(fasta)

	if len(fasta_list) > 0:
		master_list.append([filename, fasta_list])
		if not args.quiet:
			print('Removed ' + str(removed) + ' entries from ' + filename)


# output the files
for entry in master_list:
	with open('mod_' + entry[0], 'w') as outfile:
		if not args.quiet:
			print('Writing ' + str(len(entry[1])) + ' entries to new file mod_' + entry[0])
		for fasta in entry[1]:
			SeqIO.write(fasta, outfile, 'fasta')