Mercurial > repos > jjohnson > spectrast

annotate spectrast_params.py @ 2:e67b0cc10377 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
author jjohnson
date Wed, 20 Jun 2018 12:58:33 -0400
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children 7f02fc51bddf
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2
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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1 #!/usr/bin/env python
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2
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3 from __future__ import print_function
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4
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5 import argparse
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6 import re
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7 import sys
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8
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9 search_opts = [
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10 'libraryFile',
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11 'databaseFile',
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12 'databaseType',
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13 'indexCacheAll',
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14 # 'filterSelectedListFileName',
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15 'precursorMzTolerance',
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16 'precursorMzUseAverage',
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17 'searchAllCharges',
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18 'detectHomologs',
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19 'fvalFractionDelta',
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20 'useSp4Scoring',
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21 'fvalUseDotBias',
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22 'usePValue',
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23 'useTierwiseOpenModSearch',
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24 # 'expectedCysteineMod',
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25 # 'ignoreSpectraWithUnmodCysteine',
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26 # 'ignoreChargeOneLibSpectra',
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27 # 'ignoreAbnormalSpectra',
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28 'outputExtension',
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29 'outputDirectory',
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30 'hitListTopHitFvalThreshold',
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31 'hitListLowerHitsFvalThreshold',
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32 'hitListShowHomologs',
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33 'hitListShowMaxRank',
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34 'hitListOnlyTopHit',
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35 'hitListExcludeNoMatch',
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36 'enzymeForPepXMLOutput',
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37 'printFingerprintingSummary',
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38 'filterMinPeakCount',
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39 'filterAllPeaksBelowMz',
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40 'filterMaxIntensityBelow',
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41 'filterMinMzRange',
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42 'filterCountPeakIntensityThreshold',
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43 'filterRemovePeakIntensityThreshold',
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44 'filterMaxPeaksUsed',
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45 'filterMaxDynamicRange',
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46 'peakScalingMzPower',
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47 'peakScalingIntensityPower',
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48 'peakScalingUnassignedPeaks',
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49 'peakNoBinning',
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50 'peakBinningNumBinsPerMzUnit',
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51 'peakBinningFractionToNeighbor',
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52 'filterLibMaxPeaksUsed',
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53 'filterLightIonsMzThreshold',
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54 'filterITRAQReporterPeaks',
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55 'filterTMTReporterPeaks',
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56 # 'filterRemoveHuge515Threshold',
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57 ]
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58
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59
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60 def __main__():
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61 parser = argparse.ArgumentParser(
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62 description='Parse SpectraST search.params files' +
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63 ' to create an updated search.params')
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64 parser.add_argument(
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65 'param_files', nargs='*',
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66 help='A SpectraST search.params files')
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67 parser.add_argument(
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68 '-o', '--output',
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69 help='Output file (-) for stdout')
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70 args = parser.parse_args()
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71
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72 output_wtr = open(args.output, 'w')\
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73 if args.output and args.output != '-' else sys.stdout
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74
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75 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')
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76 search_params = dict()
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77
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78 # Collect all search_params
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79 def parse_params(param_file, fh):
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80 for i, line in enumerate(fh):
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81 try:
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82 m = optpat.match(line.rstrip())
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83 if m:
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84 k, v = m.groups()
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85 if k in search_opts:
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jjohnson
parents:
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86 search_params[k] = v
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jjohnson
parents:
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87 except Exception, e:
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jjohnson
parents:
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88 print('%s(%d): %s %s' % (param_file, i, line, e),
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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89 file=sys.stderr)
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jjohnson
parents:
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90
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jjohnson
parents:
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91 if args.param_files:
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jjohnson
parents:
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92 for param_file in args.param_files:
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jjohnson
parents:
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93 try:
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jjohnson
parents:
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94 with open(param_file, 'r') as fh:
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jjohnson
parents:
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95 parse_params(param_file, fh)
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jjohnson
parents:
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96 except Exception, e:
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jjohnson
parents:
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97 print('parse_params: %s' % e, file=sys.stderr)
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jjohnson
parents:
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98 else:
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jjohnson
parents:
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99 try:
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jjohnson
parents:
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100 parse_params('stdin', sys.stdin)
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jjohnson
parents:
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101 except Exception, e:
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jjohnson
parents:
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102 print('parse_params: %s' % e, file=sys.stderr)
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jjohnson
parents:
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103
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jjohnson
parents:
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104 # Write search_params
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jjohnson
parents:
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105 for search_opt in search_opts:
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jjohnson
parents:
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106 if search_opt in search_params:
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jjohnson
parents:
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107 print('%s = %s' % (search_opt, search_params[search_opt]), file=output_wtr)
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jjohnson
parents:
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108
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jjohnson
parents:
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109
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jjohnson
parents:
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110 if __name__ == "__main__":
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jjohnson
parents:
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111 __main__()