Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/CombineTags.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2011 | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 # | |
31 import os | |
32 import random | |
33 from optparse import OptionParser | |
34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer | |
35 from SMART.Java.Python.misc.Progress import Progress | |
36 from commons.core.parsing.ParserChooser import ParserChooser | |
37 from commons.core.writer.Gff3Writer import Gff3Writer | |
38 | |
39 OPERATIONS = ("plus", "minus", "times", "div") | |
40 | |
41 class CombineTags(object): | |
42 | |
43 def __init__(self, verbosity = 0): | |
44 self.verbosity = verbosity | |
45 | |
46 def setInputFile(self, fileName, format): | |
47 self.inputFileName = fileName | |
48 parserChooser = ParserChooser(self.verbosity) | |
49 parserChooser.findFormat(format, "transcript") | |
50 self.parser = parserChooser.getParser(fileName) | |
51 | |
52 def setOutputFile(self, fileName): | |
53 self.outputWriter = Gff3Writer(fileName, self.verbosity) | |
54 | |
55 def setTags(self, tag1, tag2, outputTag, defaultValue = None): | |
56 self.tag1 = tag1 | |
57 self.tag2 = tag2 | |
58 self.outputTag = outputTag | |
59 self.defaultValue = defaultValue | |
60 | |
61 def setOperation(self, operation): | |
62 self.operation = operation | |
63 if self.operation not in OPERATIONS: | |
64 raise Exception("Do no handle operation %s, only: %s" % (self.operation, ", ".join(OPERATIONS))) | |
65 | |
66 def run(self): | |
67 progress = Progress(self.parser.getNbTranscripts(), "Printing transcripts %s" % (self.inputFileName), self.verbosity) | |
68 for transcript in self.parser.getIterator(): | |
69 tag1 = transcript.getTagValue(self.tag1) | |
70 tag2 = transcript.getTagValue(self.tag2) | |
71 if tag1 == None or tag2 == None: | |
72 if self.defaultValue == None: | |
73 raise Exception("Transcript %s misses one of the tags %s and %s, and has no default value !" % (transcript, self.tag1, self.tag2)) | |
74 newTag = self.defaultValue | |
75 else: | |
76 tag1, tag2 = float(tag1), float(tag2) | |
77 if self.operation == "plus": | |
78 newTag = tag1 + tag2 | |
79 elif self.operation == "minus": | |
80 newTag = tag1 - tag2 | |
81 elif self.operation == "times": | |
82 newTag = tag1 * tag2 | |
83 elif self.operation == "div": | |
84 newTag = tag1 / tag2 | |
85 transcript.setTagValue(self.outputTag, newTag) | |
86 self.outputWriter.addTranscript(transcript) | |
87 progress.inc() | |
88 progress.done() | |
89 self.parser.close() | |
90 self.outputWriter.close() | |
91 | |
92 | |
93 if __name__ == "__main__": | |
94 | |
95 # parse command line | |
96 description = "Change Tag Name v1.0.1: Change the name of tag of a list of transcripts. [Category: Data Modification]" | |
97 | |
98 parser = OptionParser(description = description) | |
99 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") | |
100 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]") | |
101 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]") | |
102 parser.add_option("-t", "--tag1", dest="tag1", action="store", type="string", help="name of the first tag [compulsory] [format: string]") | |
103 parser.add_option("-T", "--tag2", dest="tag2", action="store", type="string", help="name of the second tag [compulsory] [format: string]") | |
104 parser.add_option("-d", "--default", dest="defaultValue", action="store", default=None, type="string", help="default value when one of the tag is absent [compulsory] [format: float]") | |
105 parser.add_option("-n", "--new", dest="newTag", action="store", type="string", help="name of the new tag [compulsory] [format: string]") | |
106 parser.add_option("-p", "--operation", dest="operation", action="store", type="string", help="operation combining the tags [compulsory] [format: choice (plus, minus, times, div)]") | |
107 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") | |
108 (options, args) = parser.parse_args() | |
109 | |
110 combiner = CombineTags(options.verbosity) | |
111 combiner.setInputFile(options.inputFileName, options.inputFormat) | |
112 combiner.setOutputFile("%s.gff3" % (options.outputFileName)) | |
113 combiner.setTags(options.tag1, options.tag2, options.newTag, options.defaultValue) | |
114 combiner.setOperation(options.operation) | |
115 combiner.run() |