Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/CombineTags.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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()