splitFASTA.py

'''
	Split file containing multiple FASTA genomes into separate files.
	Header line will form new file name. Default output directory is current directory.
'''

import argparse
import os
import sys


def split(filename, output_dir):
    rx = r'>(.)'
    current_file = None
    with open(str(filename), 'r') as f:
        for line in f.readlines():
            if (line.startswith(">")):
                pos = line.rfind('|')
                filename_new = os.path.join(output_dir, line[1:pos].rstrip() + '.fasta')
                print "pos = " + str(pos) + ", filename = " + filename_new
                if (current_file is not None):
                    current_file.close()
                print "writing to current_file = " + filename_new
                current_file = open(filename_new, 'w')

            current_file.write(line)


if __name__ == "__main__":

    parser = argparse.ArgumentParser(description='Split file of multiple FASTA genomes into separate files.')
    parser.add_argument('filename', type=str, help='give file name')
    parser.add_argument('-o', dest='output_dir', type=str, default='.', help='give output directory')
    args = parser.parse_args()
    if os.path.isfile(str(args.filename)) is False:
        print('input file does not exist: ' + str(args.filename))
        sys.exit(0)
    if os.path.isdir(args.output_dir) is False:
        print('output directory does not exist: ' + args.output_dir)
        sys.exit(0)
    split(args.filename, args.output_dir)