Search for a sequence in a FASTA file

search.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Search for a sequence in a FASTA file
# Author: Lior Galanti < [email protected] >
# NYU Center for Genetics and System Biology 2015
#
# search 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 2 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 io
import sys
from io import StringIO

def usage():
    print('usage: path query')

def search(path, query):
    reference = StringIO()
    with io.open(path, 'r') as file:
        try:
            for line in file:
                line = line.strip()
                if line[0] != '>':
                    reference.write(line)
            reference.seek(0)
            reference = reference.getvalue()
            start = reference.find(query)
            while start >= 0:
                end = start + len(query)
                print('{}:{}'.format(start, end))
                start = reference.find(query, start + 1)
                
        except OSError as e:
            print('{} {}'.format(e.strerror, path))

if len(sys.argv) > 1:
    path = sys.argv[1]
    query = sys.argv[2]
    search(path, query)