view @ 1:8acb72264319 draft default tip

planemo upload for repository commit 55671fc041c29c7985cbb44e6b49a10e1889f907
author drosofff
date Mon, 21 Mar 2016 18:03:40 -0400
parents 55107d4a728c
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line source

import sys
import argparse

def Parser():
    the_parser = argparse.ArgumentParser()
        '--input', action="store", type=str, help="input SAM file")
        '--output', action="store", type=str, help="output FASTQ file")
    args = the_parser.parse_args()
    return args
def print_fastq_sequence(samline, file):
  samfields = samline[:-1].split("\t")
  file.write ( '@%s\n%s\n+\n%s\n' % (samfields[0], samfields[9], samfields[10]) )

def main(input, output):
    infile = open (input, "r")
    outfile = open (output, "w")
    with open (input, "r") as infile:
        with open (output, "w") as outfile:
            for line in infile:
                if line[0] == "@":
                if line.split("\t")[1] != "4":
                    print_fastq_sequence (line, outfile)

if __name__ == "__main__":
    args = Parser()
    main (args.input, args.output)