Mercurial > repos > bgruening > unique
comparison uniq.py @ 0:4382d742830f draft
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| author | bgruening |
|---|---|
| date | Mon, 26 Aug 2013 04:38:43 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:4382d742830f |
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| 1 import sys | |
| 2 import subprocess | |
| 3 | |
| 4 """ | |
| 5 We only need that file because galaxy do not understand the -t $'\t' term. | |
| 6 Otherwise that would be the right XML-only solution: | |
| 7 sort -u | |
| 8 $ignore_case | |
| 9 $is_numeric | |
| 10 -t \$'\t' | |
| 11 #if $adv_opts.adv_opts_selector=="advanced": | |
| 12 -k$adv_opts.column_start,$adv_opts.column_end | |
| 13 #end if | |
| 14 -o $outfile | |
| 15 $input | |
| 16 """ | |
| 17 | |
| 18 if sys.argv[1].strip() != 'false': | |
| 19 ignore_case = sys.argv[1] | |
| 20 else: | |
| 21 ignore_case = '' | |
| 22 | |
| 23 if sys.argv[2].strip() != 'false': | |
| 24 is_numeric = sys.argv[2] | |
| 25 else: | |
| 26 is_numeric = '' | |
| 27 | |
| 28 try: | |
| 29 col_start = sys.argv[3] | |
| 30 col_end = sys.argv[4] | |
| 31 com = "sort -u %s %s -t ' ' -k%s,%s -o %s %s" % (is_numeric, ignore_case, col_start, col_end, sys.argv[5], sys.argv[6]) | |
| 32 except: | |
| 33 # no advanced options selected | |
| 34 com = "sort -u %s %s -t ' ' -o %s %s" % (is_numeric, ignore_case, sys.argv[3], sys.argv[4]) | |
| 35 | |
| 36 subprocess.call(com, shell=True) |