comparison sam_to_fastq.py @ 0:4c60ceadc414 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty

0:4c60ceadc414

#!/usr/bin/python
#
import sys
import argparse

def Parser():
    the_parser = argparse.ArgumentParser()
    the_parser.add_argument(
        '--input', action="store", type=str, help="input SAM file")
    the_parser.add_argument(
        '--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")
  print >> file, '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10])

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

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