Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/clusterize.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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children | 169d364ddd91 |
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35:d94018ca4ada | 36:44d5973c188c |
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1 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2010 | |
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 from commons.core.writer.WriterChooser import WriterChooser | |
32 """Clusterize a set of transcripts""" | |
33 | |
34 import os, os.path, random | |
35 from optparse import OptionParser | |
36 from commons.core.parsing.ParserChooser import ParserChooser | |
37 from commons.core.writer.Gff3Writer import Gff3Writer | |
38 from SMART.Java.Python.structure.Transcript import Transcript | |
39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle | |
40 from SMART.Java.Python.ncList.FileSorter import FileSorter | |
41 from SMART.Java.Python.misc.Progress import Progress | |
42 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress | |
43 | |
44 class Clusterize(object): | |
45 | |
46 def __init__(self, verbosity): | |
47 self.normalize = False | |
48 self.presorted = False | |
49 self.distance = 1 | |
50 self.colinear = False | |
51 self.nbWritten = 0 | |
52 self.nbMerges = 0 | |
53 self.verbosity = verbosity | |
54 self.splittedFileNames = {} | |
55 | |
56 def __del__(self): | |
57 for fileName in self.splittedFileNames.values(): | |
58 os.remove(fileName) | |
59 | |
60 def setInputFile(self, fileName, format): | |
61 parserChooser = ParserChooser(self.verbosity) | |
62 parserChooser.findFormat(format) | |
63 self.parser = parserChooser.getParser(fileName) | |
64 self.sortedFileName = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000)) | |
65 if "SMARTTMPPATH" in os.environ: | |
66 self.sortedFileName = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileName)) | |
67 | |
68 def setOutputFileName(self, fileName, format="gff3", title="S-MART", feature="transcript", featurePart="exon"): | |
69 writerChooser = WriterChooser() | |
70 writerChooser.findFormat(format) | |
71 self.writer = writerChooser.getWriter(fileName) | |
72 self.writer.setTitle(title) | |
73 self.writer.setFeature(feature) | |
74 self.writer.setFeaturePart(featurePart) | |
75 | |
76 def setDistance(self, distance): | |
77 self.distance = distance | |
78 | |
79 def setColinear(self, colinear): | |
80 self.colinear = colinear | |
81 | |
82 def setNormalize(self, normalize): | |
83 self.normalize = normalize | |
84 | |
85 def setPresorted(self, presorted): | |
86 self.presorted = presorted | |
87 | |
88 def _sortFile(self): | |
89 if self.presorted: | |
90 return | |
91 fs = FileSorter(self.parser, self.verbosity-4) | |
92 fs.perChromosome(True) | |
93 fs.setPresorted(self.presorted) | |
94 fs.setOutputFileName(self.sortedFileName) | |
95 fs.sort() | |
96 self.splittedFileNames = fs.getOutputFileNames() | |
97 self.nbElementsPerChromosome = fs.getNbElementsPerChromosome() | |
98 self.nbElements = fs.getNbElements() | |
99 | |
100 def _iterate(self, chromosome): | |
101 if chromosome == None: | |
102 progress = UnlimitedProgress(10000, "Reading input file", self.verbosity) | |
103 parser = self.parser | |
104 else: | |
105 progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity) | |
106 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity) | |
107 transcripts = [] | |
108 self.nbElements = 0 | |
109 for newTranscript in parser.getIterator(): | |
110 newTranscripts = [] | |
111 if newTranscript.__class__.__name__ == "Mapping": | |
112 newTranscript = newTranscript.getTranscript() | |
113 for oldTranscript in transcripts: | |
114 if self._checkOverlap(newTranscript, oldTranscript): | |
115 self._merge(newTranscript, oldTranscript) | |
116 elif self._checkPassed(newTranscript, oldTranscript): | |
117 self._write(oldTranscript) | |
118 else: | |
119 newTranscripts.append(oldTranscript) | |
120 newTranscripts.append(newTranscript) | |
121 transcripts = newTranscripts | |
122 self.nbElements += 1 | |
123 progress.inc() | |
124 for transcript in transcripts: | |
125 self._write(transcript) | |
126 progress.done() | |
127 | |
128 def _merge(self, transcript1, transcript2): | |
129 self.nbMerges += 1 | |
130 transcript2.setDirection(transcript1.getDirection()) | |
131 transcript1.merge(transcript2) | |
132 | |
133 def _write(self, transcript): | |
134 self.nbWritten += 1 | |
135 self.writer.addTranscript(transcript) | |
136 | |
137 def _checkOverlap(self, transcript1, transcript2): | |
138 if transcript1.getChromosome() != transcript2.getChromosome(): | |
139 return False | |
140 if self.colinear and transcript1.getDirection() != transcript2.getDirection(): | |
141 return False | |
142 if transcript1.getDistance(transcript2) > self.distance: | |
143 return False | |
144 return True | |
145 | |
146 def _checkPassed(self, transcript1, transcript2): | |
147 return ((transcript1.getChromosome() != transcript2.getChromosome()) or (transcript1.getDistance(transcript2) > self.distance)) | |
148 | |
149 def run(self): | |
150 self._sortFile() | |
151 if self.presorted: | |
152 self._iterate(None) | |
153 else: | |
154 for chromosome in sorted(self.splittedFileNames.keys()): | |
155 self._iterate(chromosome) | |
156 self.writer.close() | |
157 if self.verbosity > 0: | |
158 print "# input: %d" % (self.nbElements) | |
159 print "# written: %d (%d%% overlaps)" % (self.nbWritten, 0 if (self.nbElements == 0) else ((float(self.nbWritten) / self.nbElements) * 100)) | |
160 print "# merges: %d" % (self.nbMerges) | |
161 | |
162 | |
163 if __name__ == "__main__": | |
164 description = "Clusterize v1.0.3: clusterize the data which overlap. [Category: Merge]" | |
165 | |
166 parser = OptionParser(description = description) | |
167 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") | |
168 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: transcript file format]") | |
169 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in transcript format given by -u]") | |
170 parser.add_option("-u", "--outputFormat", dest="outputFormat", action="store", default="gff", type="string", help="output file format [format: transcript file format]") | |
171 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="merge colinear transcripts only [format: bool] [default: false]") | |
172 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts to be merged [format: int] [default: 0]") | |
173 parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]") | |
174 parser.add_option("-s", "--sorted", dest="sorted", action="store_true", default=False, help="input is already sorted [format: bool] [default: false]") | |
175 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") | |
176 (options, args) = parser.parse_args() | |
177 | |
178 c = Clusterize(options.verbosity) | |
179 c.setInputFile(options.inputFileName, options.format) | |
180 c.setOutputFileName(options.outputFileName, options.outputFormat) | |
181 c.setColinear(options.colinear) | |
182 c.setDistance(options.distance) | |
183 c.setNormalize(options.normalize) | |
184 c.setPresorted(options.sorted) | |
185 c.run() |