Mercurial > repos > jjohnson > spectrast

comparison spectrast_params.py @ 3:7f02fc51bddf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
author jjohnson
date Wed, 25 Jul 2018 10:58:17 -0400
parents e67b0cc10377
children c9bfe6adb7cd
comparison
equal deleted inserted replaced
2:e67b0cc10377 3:7f02fc51bddf
3 from __future__ import print_function 3 from __future__ import print_function
4 4
5 import argparse 5 import argparse
6 import re 6 import re
7 import sys 7 import sys
8
9 create_opts = [
10 'outputFileName',
11 'useProbTable',
12 'useProteinList',
13 'printMRMTable',
14 'remark',
15 'binaryFormat',
16 'writeDtaFiles',
17 'writeMgfFiles',
18 'removeDecoyProteins',
19 'plotSpectra',
20 'minimumProbabilityToInclude',
21 'maximumFDRToInclude',
22 'datasetName',
23 'setFragmentation',
24 'setDeamidatedNXST',
25 'addMzXMLFileToDatasetName',
26 'centroidPeaks',
27 'rawSpectraNoiseThreshold',
28 'rawSpectraMaxDynamicRange',
29 'minimumNumAAToInclude',
30 'minimumNumPeaksToInclude',
31 'skipRawAnnotation',
32 'minimumDeltaCnToInclude',
33 'maximumMassDiffToInclude',
34 'bracketSpectra',
35 'mergeBracket',
36 'filterCriteria',
37 'combineAction',
38 'buildAction',
39 'refreshDatabase',
40 'reduceSpectra',
41 'refreshDeleteUnmapped',
42 'refreshDeleteMultimapped',
43 'reannotatePeaks',
44 'minimumNumPeaksToInclude',
45 'minimumMRMQ3MZ',
46 'maximumMRMQ3MZ',
47 'minimumNumPeaksToInclude',
48 'refreshTrypticOnly',
49 'minimumNumReplicates',
50 'removeDissimilarReplicates',
51 'peakQuorum',
52 'maximumNumPeaksUsed',
53 'maximumNumReplicates',
54 'maximumNumPeaksKept',
55 'replicateWeight',
56 'recordRawSpectra',
57 'minimumNumReplicates',
58 'qualityLevelRemove,',
59 'qualityPenalizeSingletons',
60 'qualityImmuneProbThreshold',
61 'qualityImmuneMultipleEngines',
62 'useBayesianDenoiser',
63 'trainBayesianDenoiser',
64 'denoiserMinimumSignalProb',
65 'denoiserParamFile',
66 'decoyConcatenate',
67 'decoySizeRatio',
68 'decoyPrecursorSwap',
69 'normalizeRTWithLandmarks',
70 'normalizeRTLinearRegression',
71 'unidentifiedClusterIndividualRun',
72 'unidentifiedClusterMinimumDot',
73 'unidentifiedRemoveSinglyCharged',
74 'unidentifiedMinimumNumPeaksToInclude',
75 'unidentifiedSingletonXreaThreshold',
76 'allowableModTokens'
77 ]
78
79 filter_opts = [
80 'outputFileName',
81 'useProbTable',
82 'useProteinList',
83 'printMRMTable',
84 'remark',
85 'binaryFormat',
86 'writeDtaFiles',
87 'writeMgfFiles',
88 'removeDecoyProteins',
89 'plotSpectra',
90 'minimumProbabilityToInclude',
91 'maximumFDRToInclude',
92 'datasetName',
93 'setFragmentation',
94 'setDeamidatedNXST',
95 'addMzXMLFileToDatasetName',
96 'centroidPeaks',
97 'rawSpectraNoiseThreshold',
98 'rawSpectraMaxDynamicRange',
99 'minimumNumAAToInclude',
100 'minimumNumPeaksToInclude',
101 'skipRawAnnotation',
102 'minimumDeltaCnToInclude',
103 'maximumMassDiffToInclude',
104 'bracketSpectra',
105 'mergeBracket',
106 'filterCriteria',
107 'combineAction',
108 'buildAction',
109 'refreshDatabase',
110 'reduceSpectra',
111 'refreshDeleteUnmapped',
112 'refreshDeleteMultimapped',
113 'reannotatePeaks',
114 'minimumNumPeaksToInclude',
115 'minimumMRMQ3MZ',
116 'maximumMRMQ3MZ',
117 'minimumNumPeaksToInclude',
118 'refreshTrypticOnly',
119 'minimumNumReplicates',
120 'removeDissimilarReplicates',
121 'peakQuorum',
122 'maximumNumPeaksUsed',
123 'maximumNumReplicates',
124 'maximumNumPeaksKept',
125 'replicateWeight',
126 'recordRawSpectra',
127 'minimumNumReplicates',
128 'qualityLevelRemove,',
129 'qualityPenalizeSingletons',
130 'qualityImmuneProbThreshold',
131 'qualityImmuneMultipleEngines',
132 'useBayesianDenoiser',
133 'trainBayesianDenoiser',
134 'denoiserMinimumSignalProb',
135 'denoiserParamFile',
136 'decoyConcatenate',
137 'decoySizeRatio',
138 'decoyPrecursorSwap',
139 'normalizeRTWithLandmarks',
140 'normalizeRTLinearRegression',
141 'unidentifiedClusterIndividualRun',
142 'unidentifiedClusterMinimumDot',
143 'unidentifiedRemoveSinglyCharged',
144 'unidentifiedMinimumNumPeaksToInclude',
145 'unidentifiedSingletonXreaThreshold',
146 'allowableModTokens'
147 ]
8 148
9 search_opts = [ 149 search_opts = [
10 'libraryFile', 150 'libraryFile',
11 'databaseFile', 151 'databaseFile',
12 'databaseType', 152 'databaseType',
63 ' to create an updated search.params') 203 ' to create an updated search.params')
64 parser.add_argument( 204 parser.add_argument(
65 'param_files', nargs='*', 205 'param_files', nargs='*',
66 help='A SpectraST search.params files') 206 help='A SpectraST search.params files')
67 parser.add_argument( 207 parser.add_argument(
208 '-m', '--mode', choices=['search','create','filter'],
209 help='')
210 parser.add_argument(
68 '-o', '--output', 211 '-o', '--output',
69 help='Output file (-) for stdout') 212 help='Output file (-) for stdout')
70 args = parser.parse_args() 213 args = parser.parse_args()
71 214
72 output_wtr = open(args.output, 'w')\ 215 output_wtr = open(args.output, 'w')\
73 if args.output and args.output != '-' else sys.stdout 216 if args.output and args.output != '-' else sys.stdout
74 217
75 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$') 218 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')
76 search_params = dict() 219
77 220 valid_opts = search_opts if args.mode == 'search' else create_opts if args.mode == 'create' else filter_opts
78 # Collect all search_params 221 valid_params = dict()
79 def parse_params(param_file, fh): 222
223 # Collect all valid_params
224 def parse_params(param_file, fh, valid_opts):
80 for i, line in enumerate(fh): 225 for i, line in enumerate(fh):
81 try: 226 try:
82 m = optpat.match(line.rstrip()) 227 m = optpat.match(line.rstrip())
83 if m: 228 if m:
84 k, v = m.groups() 229 k, v = m.groups()
85 if k in search_opts: 230 if k in valid_opts:
86 search_params[k] = v 231 valid_params[k] = v
87 except Exception, e: 232 except Exception, e:
88 print('%s(%d): %s %s' % (param_file, i, line, e), 233 print('%s(%d): %s %s' % (param_file, i, line, e),
89 file=sys.stderr) 234 file=sys.stderr)
90 235
91 if args.param_files: 236 if args.param_files:
92 for param_file in args.param_files: 237 for param_file in args.param_files:
93 try: 238 try:
94 with open(param_file, 'r') as fh: 239 with open(param_file, 'r') as fh:
95 parse_params(param_file, fh) 240 parse_params(param_file, fh, valid_opts)
96 except Exception, e: 241 except Exception, e:
97 print('parse_params: %s' % e, file=sys.stderr) 242 print('parse_params: %s' % e, file=sys.stderr)
98 else: 243 else:
99 try: 244 try:
100 parse_params('stdin', sys.stdin) 245 parse_params('stdin', sys.stdin)
101 except Exception, e: 246 except Exception, e:
102 print('parse_params: %s' % e, file=sys.stderr) 247 print('parse_params: %s' % e, file=sys.stderr)
103 248
104 # Write search_params 249 # Write valid_params
105 for search_opt in search_opts: 250 for valid_opt in valid_opts:
106 if search_opt in search_params: 251 if valid_opt in valid_params:
107 print('%s = %s' % (search_opt, search_params[search_opt]), file=output_wtr) 252 print('%s = %s' % (valid_opt, valid_params[valid_opt]), file=output_wtr)
108 253
109 254
110 if __name__ == "__main__": 255 if __name__ == "__main__":
111 __main__() 256 __main__()
257