Mercurial > repos > galaxyp > hardklor
comparison hardklor.py @ 0:d796e6613d19 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
| author | galaxyp |
|---|---|
| date | Mon, 23 May 2016 11:12:40 -0400 |
| parents | |
| children | 73fc27617b2e |
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| -1:000000000000 | 0:d796e6613d19 |
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| 1 """ | |
| 2 Usage: | |
| 3 python hardklor.py ms1extenstion ms2extension ms1file | |
| 4 ms2file outputfile | |
| 5 """ | |
| 6 import sys | |
| 7 import os | |
| 8 import subprocess | |
| 9 | |
| 10 | |
| 11 CONFIG_FILE = 'hk.conf' | |
| 12 extension_lookup = { | |
| 13 'mzml' : 'mzML', | |
| 14 'mzxml' : 'mzXML', | |
| 15 'ms1' : 'MS1', | |
| 16 } | |
| 17 | |
| 18 # input: | |
| 19 ms1_ext = sys.argv[1] | |
| 20 ms1_file = sys.argv[2] | |
| 21 output_file = sys.argv[3] | |
| 22 config_load = os.path.join(os.path.split(sys.argv[0])[0], 'hardklor.conf') | |
| 23 | |
| 24 # parse options | |
| 25 options = {} | |
| 26 for arg in [x.split('=') for x in sys.argv[4:]]: | |
| 27 if arg[1] != '': | |
| 28 options[arg[0].replace('-', '')] = arg[1] | |
| 29 | |
| 30 | |
| 31 # create softlinks since hardklor needs "proper" extensions for input files | |
| 32 if ms1_ext in extension_lookup: | |
| 33 ms1_ext = extension_lookup[ms1_ext] | |
| 34 linkname = 'ms1_dsetlink.{0}'.format(ms1_ext) | |
| 35 os.symlink(ms1_file, linkname) | |
| 36 ms1_file = linkname | |
| 37 | |
| 38 # load template and dump to config file | |
| 39 with open(config_load) as fp: | |
| 40 config_str = fp.read() | |
| 41 config_to_dump = config_str.format( | |
| 42 instrument=options['instrument'], | |
| 43 resolution=options['resolution'], | |
| 44 centroided=options['centroided'], | |
| 45 mslvl=options['mslvl'], | |
| 46 depth=options['depth'], | |
| 47 algorithm=options['algorithm'], | |
| 48 charge_algo=options['charge_algo'], | |
| 49 mincharge=options['mincharge'], | |
| 50 maxcharge=options['maxcharge'], | |
| 51 correlation=options['correlation'], | |
| 52 sensitivity=options['sensitivity'], | |
| 53 maxfeat=options['maxfeat'], | |
| 54 inputfile=ms1_file, | |
| 55 outputfile=output_file, | |
| 56 ) | |
| 57 with open(CONFIG_FILE, 'w') as fp: | |
| 58 fp.write(config_to_dump) | |
| 59 | |
| 60 # Run hardklor | |
| 61 err = subprocess.call(['hardklor', CONFIG_FILE]) | |
| 62 sys.exit(err) |