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annotate hardklor.py @ 6:f416698530c3 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
author galaxyp
date Tue, 07 Apr 2020 07:22:58 +0000
parents b192c8c3e77e
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b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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1 """
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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2 Usage:
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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3 python hardklor.py ms1extenstion ms2extension ms1file
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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4 ms2file outputfile
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5 """
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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6 import sys
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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7 import os
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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8 import subprocess
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b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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11 CONFIG_FILE = 'hk.conf'
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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12 extension_lookup = {
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f416698530c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
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13 'mzml': 'mzML',
f416698530c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
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14 'mzxml': 'mzXML',
f416698530c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
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15 'ms1': 'MS1',
f416698530c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
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16 }
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18 # input:
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19 ms1_ext = sys.argv[1]
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20 ms1_file = sys.argv[2]
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21 output_file = sys.argv[3]
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22 config_load = os.path.join(os.path.split(sys.argv[0])[0], 'hardklor.conf')
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24 # parse options
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25 options = {}
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26 for arg in [x.split('=') for x in sys.argv[4:]]:
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27 if arg[1] != '':
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28 options[arg[0].replace('-', '')] = arg[1]
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31 # create softlinks since hardklor needs "proper" extensions for input files
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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32 if ms1_ext in extension_lookup:
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33 ms1_ext = extension_lookup[ms1_ext]
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34 linkname = 'ms1_dsetlink.{0}'.format(ms1_ext)
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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35 os.symlink(ms1_file, linkname)
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36 ms1_file = linkname
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38 # load template and dump to config file
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39 with open(config_load) as fp:
b192c8c3e77e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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40 config_str = fp.read()
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41 config_to_dump = config_str.format(
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42 instrument=options['instrument'],
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43 resolution=options['resolution'],
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44 centroided=options['centroided'],
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45 mslvl=options['mslvl'],
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46 depth=options['depth'],
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47 algorithm=options['algorithm'],
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48 charge_algo=options['charge_algo'],
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49 mincharge=options['mincharge'],
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50 maxcharge=options['maxcharge'],
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51 correlation=options['correlation'],
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52 sensitivity=options['sensitivity'],
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53 maxfeat=options['maxfeat'],
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54 inputfile=ms1_file,
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55 outputfile=output_file,
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56 )
0
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57 with open(CONFIG_FILE, 'w') as fp:
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58 fp.write(config_to_dump)
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59
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60 # Run hardklor
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61 err = subprocess.call(['hardklor', CONFIG_FILE])
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62 sys.exit(err)