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comparison smart_toolShed/SMART/Java/Python/getRandomRegions.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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 """Find random regions in a genome"""
32
33 import random, math
34 from optparse import OptionParser
35 from commons.core.parsing.FastaParser import *
36 from commons.core.writer.Gff3Writer import *
37 from commons.core.writer.MySqlTranscriptWriter import *
38 from SMART.Java.Python.misc.Progress import *
39 from SMART.Java.Python.structure.Transcript import Transcript
40 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
41
42 repetitions = 100
43
44
45 class RandomRegionsGenerator(object):
46
47 def __init__(self, verbosity):
48 self.verbosity = verbosity
49 self.strands = False
50 self.distribution = "uniform"
51 self.transcripts = None
52 self.sequenceParser = None
53 random.seed()
54
55
56 def setInput(self, fileName):
57 self.sequenceParser = FastaParser(fileName, self.verbosity)
58
59
60 def setGenomeSize(self, size):
61 self.genomeSize = size
62
63
64 def setChromosomeName(self, name):
65 self.chromosomeName = name
66
67
68 def setAnnotation(self, fileName, format):
69 parser = TranscriptContainer(fileName, format, self.verbosity)
70 self.transcripts = []
71 for transcript in parser.getIterator():
72 self.transcripts.append(transcript)
73 self.setNumber(len(self.transcripts))
74 self.setSize(0)
75
76
77 def setOutputFile(self, fileName):
78 self.outputFileName = fileName
79
80
81 def setSize(self, size):
82 self.minSize = size
83 self.maxSize = size
84
85
86 def setMinSize(self, size):
87 self.minSize = size
88
89
90 def setMaxSize(self, size):
91 self.maxSize = size
92
93
94 def setNumber(self, number):
95 self.number = number
96
97
98 def setStrands(self, strands):
99 self.strands = strands
100
101
102 def setMaxDistribution(self, maxElements):
103 if maxElements == None:
104 return
105 self.maxElements = maxElements
106 self.distribution = "gaussian"
107
108
109 def setDeviationDistribution(self, deviation):
110 if deviation == None:
111 return
112 self.deviation = deviation
113 self.distribution = "gaussian"
114
115
116 def getSizes(self):
117 if self.sequenceParser == None:
118 self.chromosomes = [self.chromosomeName]
119 self.sizes = {self.chromosomeName: self.genomeSize}
120 self.cumulatedSize = self.genomeSize
121 self.cumulatedSizes = {self.chromosomeName: self.genomeSize}
122 return
123 self.chromosomes = self.sequenceParser.getRegions()
124 self.sizes = {}
125 self.cumulatedSize = 0
126 self.cumulatedSizes = {}
127 for chromosome in self.chromosomes:
128 self.sizes[chromosome] = self.sequenceParser.getSizeOfRegion(chromosome)
129 self.cumulatedSize += self.sizes[chromosome]
130 self.cumulatedSizes[chromosome] = self.cumulatedSize
131
132
133 def findPosition(self, size = None):
134 if size == None:
135 size = random.randint(self.minSize, self.maxSize)
136 integer = random.randint(0, self.cumulatedSize)
137 for chromosome in self.chromosomes:
138 if self.cumulatedSizes[chromosome] > integer:
139 break
140 start = random.randint(1, self.sizes[chromosome] - size)
141 return (chromosome, start, size)
142
143
144 def createTranscript(self, chromosome, start, size, strand, cpt):
145 transcript = Transcript()
146 transcript.setChromosome(chromosome)
147 transcript.setStart(start)
148 transcript.setEnd(start + size-1)
149 transcript.setDirection(strand)
150 transcript.setName("rand_%d" % (cpt))
151 return transcript
152
153
154 def moveTranscript(self, chromosome, start, transcript):
155 while transcript.getEnd() + start - transcript.getStart() > self.cumulatedSizes[chromosome]:
156 chromosome, start, size = self.findPosition(transcript.getEnd() - transcript.getStart())
157 transcript.setChromosome(chromosome)
158 oldStart, oldEnd = transcript.getStart(), transcript.getEnd()
159 if transcript.getNbExons() > 1:
160 for exon in transcript.getNbExons():
161 oldExonStart, oldExonEnd = exon.getStart(), exon.getEnd()
162 exon.setStart(oldExonStart + start - oldStart)
163 exon.setEnd(oldExonEnd + start - oldStart)
164 transcript.setStart(start)
165 transcript.setEnd(oldEnd + start - oldStart)
166 return [transcript]
167
168
169 def createUniformCluster(self, chromosome, start, size, strand, cpt):
170 transcript = self.createTranscript(chromosome, start, size, strand, cpt)
171 return [transcript]
172
173
174 def findNbTranscripts(self, cpt):
175 return min(int(round(math.exp(random.random() * math.log(self.maxElements)))), self.number - cpt + 1)
176
177
178 def getDev(self):
179 deviation = 0.0
180 for j in range(repetitions):
181 deviation += random.randint(-self.deviation, self.deviation)
182 deviation /= repetitions
183 deviation = int(round(deviation))
184 return deviation
185
186
187 def createGaussianCluster(self, chromosome, start, size, strand, cpt):
188 transcripts = []
189 nbTranscripts = self.findNbTranscripts(cpt)
190 for i in range(nbTranscripts):
191 transcript = self.createTranscript(chromosome, start + self.getDev(), size + self.getDev(), strand, cpt + i)
192 transcripts.append(transcript)
193 return transcripts
194
195
196 def writeRegions(self):
197 writer = Gff3Writer(self.outputFileName, self.verbosity)
198 outputFile = open(self.outputFileName, "w")
199 progress = Progress(self.number, "Writing to %s" % (self.outputFileName), self.verbosity)
200 i = 0
201 while i < self.number:
202 chromosome, start, size = self.findPosition()
203 strand = random.choice([-1, 1]) if self.strands else 1
204 if self.transcripts != None:
205 transcripts = self.moveTranscript(chromosome, start, self.transcripts[i])
206 elif self.distribution == "uniform":
207 transcripts = self.createUniformCluster(chromosome, start, size, strand, i+1)
208 else:
209 transcripts = self.createGaussianCluster(chromosome, start, size, strand, i+1)
210 for transcript in transcripts:
211 writer.addTranscript(transcript)
212 i += 1
213 progress.inc()
214 progress.done()
215 outputFile.close()
216 writer.write()
217 writer.close()
218
219
220 def run(self):
221 self.getSizes()
222 self.writeRegions()
223
224
225 if __name__ == "__main__":
226
227 # parse command line
228 description = "Get Random Regions v1.0.2: Get some random coordinates on a genome. May use uniform or gaussian distribution (in gaussion distribution, # of element per cluster follows a power law). [Category: Other]"
229
230 parser = OptionParser(description = description)
231 parser.add_option("-r", "--reference", dest="reference", action="store", default=None, type="string", help="file that contains the sequences [format: file in FASTA format]")
232 parser.add_option("-S", "--referenceSize", dest="referenceSize", action="store", default=None, type="int", help="size of the chromosome (when no reference is given) [format: int]")
233 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="name of the chromosome (when no reference is given) [format: string]")
234 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
235 parser.add_option("-i", "--input", dest="inputFileName", action="store", default=None, type="string", help="optional file containing regions to shuffle [format: file in transcript format given by -f]")
236 parser.add_option("-f", "--format", dest="format", action="store", default=None, type="string", help="format of the previous file [format: transcript file format]")
237 parser.add_option("-s", "--size", dest="size", action="store", default=None, type="int", help="size of the regions (if no region set is provided) [format: int]")
238 parser.add_option("-z", "--minSize", dest="minSize", action="store", default=None, type="int", help="minimum size of the regions (if no region set nor a fixed size are provided) [format: int]")
239 parser.add_option("-Z", "--maxSize", dest="maxSize", action="store", default=None, type="int", help="maximum size of the regions (if no region set nor a fixed size are provided) [format: int]")
240 parser.add_option("-n", "--number", dest="number", action="store", default=None, type="int", help="number of regions (if no region set is provided) [format: int]")
241 parser.add_option("-t", "--strands", dest="strands", action="store_true", default=False, help="use both strands (if no region set is provided) [format: boolean]")
242 parser.add_option("-m", "--max", dest="max", action="store", default=None, type="int", help="max. # reads in a cluster (for Gaussian dist.) [format: int]")
243 parser.add_option("-d", "--deviation", dest="deviation", action="store", default=None, type="int", help="deviation around the center of the cluster (for Gaussian dist.) [format: int]")
244 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
245 (options, args) = parser.parse_args()
246
247 rrg = RandomRegionsGenerator(options.verbosity)
248 if options.reference == None:
249 rrg.setGenomeSize(options.referenceSize)
250 rrg.setChromosomeName(options.chromosome)
251 else:
252 rrg.setInput(options.reference)
253 rrg.setOutputFile(options.outputFileName)
254 if options.inputFileName == None:
255 if options.size != None:
256 rrg.setSize(options.size)
257 else:
258 rrg.setMinSize(options.minSize)
259 rrg.setMaxSize(options.maxSize)
260 rrg.setNumber(options.number)
261 rrg.setStrands(options.strands)
262 else:
263 rrg.setAnnotation(options.inputFileName, options.format)
264 rrg.setMaxDistribution(options.max)
265 rrg.setDeviationDistribution(options.deviation)
266 rrg.run()
267