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comparison sam_to_fastq.py @ 1:8acb72264319 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 55671fc041c29c7985cbb44e6b49a10e1889f907
author drosofff
date Mon, 21 Mar 2016 18:03:40 -0400
parents 55107d4a728c
children
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0:55107d4a728c 1:8acb72264319
13 return args 13 return args
14 14
15 15
16 def print_fastq_sequence(samline, file): 16 def print_fastq_sequence(samline, file):
17 samfields = samline[:-1].split("\t") 17 samfields = samline[:-1].split("\t")
18 file.write ( '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) ) 18 file.write ( '@%s\n%s\n+\n%s\n' % (samfields[0], samfields[9], samfields[10]) )
19 19
20 def main(input, output): 20 def main(input, output):
21 infile = open (input, "r") 21 infile = open (input, "r")
22 outfile = open (output, "w") 22 outfile = open (output, "w")
23 with open (input, "r") as infile: 23 with open (input, "r") as infile: