Mercurial > repos > galaxyp > psm_validation

annotate application.py @ 0:c634292d3468 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
author galaxyp
date Thu, 15 Oct 2020 07:44:52 +0000
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c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
galaxyp
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1 import argparse
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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2
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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3 import psmfragmentation.psmfragmentation as pf
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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4
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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5
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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6 if __name__ == "__main__":
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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7 parser = argparse.ArgumentParser(description="Run PSM Validator")
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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8 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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9 "-d",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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10 "--dbname",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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11 help="Path to mzsqlite db",
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12 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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13 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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14 "-p",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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15 "--peptides",
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16 help="Path to peptide sequence file",
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17 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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18 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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19 "-n",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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20 "--neutral",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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21 action="store_true",
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22 default=False,
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23 help="Calculate netutral loss",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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24 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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25 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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26 "-i",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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27 "--internal",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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28 action="store_true",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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29 default=False,
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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30 help="Calculate internals",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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31 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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32 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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33 "-e", "--epsilon", type=float
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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34 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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35 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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36 "-b",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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37 "--b_run",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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38 type=int,
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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39 default=2,
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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40 help="Number of consecutive b-ions"
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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41 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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42 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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43 "-y",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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44 "--y_run",
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45 type=int,
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46 default=2,
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47 help="Number of consecutive y-ions"
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48 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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49
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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50 parser.add_argument(
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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51 "-t",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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52 "--test",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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53 action="store_true",
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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54 default=False
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55 )
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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56
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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57 args = parser.parse_args()
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58
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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59 itypes = ['b', 'y']
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60 if args.neutral:
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61 itypes.extend(['b-H2O', 'b-NH3', 'y-H2O', 'y-NH3'])
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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62
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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63 if args.internal:
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64 itypes.append('M')
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65
c634292d3468 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
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66 pf.score_psms(args.dbname, args.peptides, ion_types=itypes, epsilon=args.epsilon, maxcharge=1, b_run=args.b_run, y_run=args.y_run, a_test=args.test)