#!/usr/bin/env python

################################################
# SPLIT FASTA FILES INTO ONE FILE PER SEQUENCE #
# THIS IS OPEN SOURCE CODE (YAY!)              #
################################################
# LICENSE
#    This code is licensed under the Creative Commons 3.0
#    Attribution + ShareAlike license - for details see:
#       http://creativecommons.org/licenses/by-sa/3.0/
#
# DATE: February 27th, 2014
#
# PROGRAM AUTHOR (PROGRAMMER)
#    Graham Alvare - home.cc.umanitoba.ca/~alvare
#
# CO-AUTHORS/ACKNOWLEDGEMENTS
#    Justin Zhang          - for providing me information on the SAM format,
#                            and test data to build and debug this program.
#    Dr. Brian Fristensky  - my work supervisor, and the man who introduced
#                            me to the wonderful field of bioinformatics.
#
# QUESTIONS & COMMENTS
#    If you have any questions, please contact me: alvare@cc.umanitoba.ca
#    I usually get back to people within 1-2 weekdays (weekends, I am slower)
#
#    P.S. Please also let me know of any bugs, or if you have any suggestions.
#         I am generally happy to help create new tools, or modify my existing
#         tools to make them more useful.
#
# Happy usage!

import sys, os, os.path, re, collections
from Bio import SeqIO

if __name__=="__main__":
	if len(sys.argv) > 1:
		# process every file specified on the command line
		for filename in sys.argv[1:]:
			# Open the FASTA file
			handle = open(filename, 'rU')

			# the sequence record number
			number = 1

			# Open output FASTA file
			for record in SeqIO.parse(handle, 'fasta'):
				outname = os.path.basename(filename) + ".seq" + str(number)
				outfile = open(outname, 'w')
				print >> outfile, "> " + str(record.id)
				print >> outfile, str(record.seq)
				outfile.close()
				number += 1

			# Close the input file handle
			handle.close()