Mercurial > repos > tiagoantao > clone_filter
diff STACKS_clone_filter.py @ 8:a8b87bc0c3ad draft
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
author | tiagoantao |
---|---|
date | Thu, 04 Feb 2016 08:13:32 -0500 |
parents | 1a5ebb16aaea |
children | 92ba49d68ef1 |
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--- a/STACKS_clone_filter.py Thu Feb 04 08:00:32 2016 -0500 +++ b/STACKS_clone_filter.py Thu Feb 04 08:13:32 2016 -0500 @@ -10,10 +10,19 @@ def __main__(): parser = argparse.ArgumentParser() + + #files (single or pair) parser.add_argument('-f', type=str) parser.add_argument('-fwd', type=str) parser.add_argument('-rev', type=str) + #oligos + parser.add_argument('-oligo_len_1', type=int) + parser.add_argument('-oligo_len_2', type=int) + + #options (allways there) + parser.add_argument('-opt', type=str) + #parser.add_argument('-k', action='store_true') options = parser.parse_args() @@ -30,6 +39,12 @@ cmd_line.extend(['-1', options.fwd]) cmd_line.extend(['-2', options.rev]) + if options.oligo_len_1 > -1: + cmd_line.extend(['--oligo_len_1', options.oligo_len_1]) + if options.oligo_len_2 > -1: + cmd_line.extend(['--oligo_len_2', options.oligo_len_2]) + cmd_line.append('--' + options.oligo_len_2) + print "[CMD]:"+' '.join(cmd_line) subprocess.call(cmd_line)