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comparison smart_toolShed/SMART/Java/Python/getWigProfile.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 """
32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
33 """
34
35 import math
36 from optparse import OptionParser
37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
38 from commons.core.parsing.WigParser import WigParser
39 from SMART.Java.Python.misc.Progress import Progress
40 from SMART.Java.Python.misc.RPlotter import RPlotter
41
42 class GetWigProfile(object):
43
44 def __init__(self, verbosity):
45 self.verbosity = verbosity
46 self.values = {}
47 self.defaultValue = 0.0
48
49 def _iToJ(self, i, size):
50 return min(self.nbPoints+1, int(math.floor(float(i - self.distance) / (size) * (self.nbPoints))))
51
52 def readTranscripts(self):
53 self.strandNames = (1, -1) if self.strands else (1, )
54 self.values = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
55 transcriptParser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
56 wigParser = WigParser(self.wig)
57 nbValues = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
58 wigParser.setStrands(self.strands)
59 wigParser.setDefaultValue(self.defaultValue)
60
61 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (self.inputFileName), self.verbosity)
62 for transcript in transcriptParser.getIterator():
63 transcriptSize = transcript.getSize()
64 expectedSize = transcriptSize + 2 * self.distance
65 transcript.extendStart(self.distance)
66 transcript.extendEnd(self.distance)
67 theseValues = transcript.extractWigData(wigParser)
68
69 if len(self.strandNames) == 1:
70 theseValues = {1: theseValues}
71 for strand in self.strandNames:
72 if len(theseValues[strand]) < expectedSize:
73 theseValues[strand] = [self.defaultValue] * (expectedSize - len(theseValues[strand])) + theseValues[strand]
74 if len(theseValues[strand]) != expectedSize:
75 raise Exception("Got something wrong with the size of the WIG data concerning %s [%s]: %d found instead of %d" % (transcript, ",".join(["%d-%d" % (exon.getStart(), exon.getEnd()) for exon in transcript.getExons()]), len(theseValues[strand]), expectedSize))
76 fivePValues = theseValues[strand][: self.distance]
77 nbValues = [0.0] * (self.nbPoints)
78 transcriptValues = [0.0] * (self.nbPoints)
79 for i in range(self.distance, len(theseValues[strand]) - self.distance):
80 startJ = self._iToJ(i, transcriptSize)
81 endJ = max(startJ+1, self._iToJ(i+1, transcriptSize))
82 for j in range(startJ, endJ):
83 transcriptValues[j] += theseValues[strand][i]
84 nbValues[j] += 1
85 threePValues = theseValues[strand][-self.distance: ]
86 values = fivePValues + [self.defaultValue if nbValue == 0 else transcriptValue / nbValue for transcriptValue, nbValue in zip(transcriptValues, nbValues)] + threePValues
87 for i, value in enumerate(values):
88 self.values[strand][i] += value
89 progress.inc()
90 progress.done()
91
92 for strand in self.strandNames:
93 if strand == 0:
94 strand = 1
95 for i in range(self.nbPoints + 2 * self.distance):
96 self.values[strand][i] /= transcriptParser.getNbTranscripts() * strand
97
98
99 def smoothen(self):
100 if self.smoothenForce == None:
101 return
102 for strand in self.strandNames:
103 averageValues = {}
104 for center in range(self.distance, self.distance + self.nbPoints):
105 sum = 0.0
106 nbValues = 0.0
107 for i in range(center - self.smoothenForce + 1, center + self.smoothenForce):
108 if i > self.distance and i < self.distance + self.nbPoints:
109 nbValues += 1
110 sum += self.values[strand][i]
111 averageValues[center] = sum / nbValues
112 for position in range(self.distance, self.distance + self.nbPoints):
113 self.values[strand][position] = averageValues[position]
114
115
116 def plot(self):
117 plotter = RPlotter(self.outputFileName, self.verbosity)
118 for strand in self.strandNames:
119 plotter.addLine(self.values[strand])
120 if self.log:
121 plotter.setLog("y")
122 plotter.setAxisLabel("x", {0: -self.distance, self.distance: "start", self.distance+self.nbPoints-1: "end", 2*self.distance+self.nbPoints-1: self.distance})
123 plotter.plot()
124
125
126
127 if __name__ == "__main__":
128
129 # parse command line
130 description = "Get WIG Profile v1.0.1: Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"
131
132 parser = OptionParser(description = description)
133 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
134 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
135 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
136 parser.add_option("-p", "--nbPoints", dest="nbPoints", action="store", default=1000, type="int", help="number of points on the x-axis [compulsory] [format: int] [default: 1000]")
137 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="distance around genomic coordinates [compulsory] [format: int] [default: 0]")
138 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
139 parser.add_option("-m", "--smoothen", dest="smoothen", action="store", default=None, type="int", help="smoothen the curve [format: int] [default: None]")
140 parser.add_option("-a", "--default", dest="defaultValue", action="store", default=0.0, type="float", help="default value (when value is NA) [default: 0.0] [format: float]")
141 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
142 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
143 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
144 (options, args) = parser.parse_args()
145
146 wigProfile = GetWigProfile(options.verbosity)
147 wigProfile.strands = options.strands
148 wigProfile.inputFileName = options.inputFileName
149 wigProfile.inputFormat = options.inputFormat
150 wigProfile.wig = options.wig
151 wigProfile.nbPoints = options.nbPoints
152 wigProfile.distance = options.distance
153 wigProfile.smoothenForce = options.smoothen
154 wigProfile.defaultValue = options.defaultValue
155 wigProfile.outputFileName = options.outputFileName
156 wigProfile.log = options.log
157
158 wigProfile.readTranscripts()
159 wigProfile.smoothen()
160 wigProfile.plot()