Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/getWigProfile.py @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
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0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
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27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 """
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34
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35 import math
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36 from optparse import OptionParser
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37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 from commons.core.parsing.WigParser import WigParser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 from SMART.Java.Python.misc.Progress import Progress
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40 from SMART.Java.Python.misc.RPlotter import RPlotter
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41
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42 class GetWigProfile(object):
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43
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44 def __init__(self, verbosity):
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45 self.verbosity = verbosity
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46 self.values = {}
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47 self.defaultValue = 0.0
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48
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49 def _iToJ(self, i, size):
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50 return min(self.nbPoints+1, int(math.floor(float(i - self.distance) / (size) * (self.nbPoints))))
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51
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52 def readTranscripts(self):
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53 self.strandNames = (1, -1) if self.strands else (1, )
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54 self.values = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
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55 transcriptParser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
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56 wigParser = WigParser(self.wig)
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57 nbValues = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
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58 wigParser.setStrands(self.strands)
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59 wigParser.setDefaultValue(self.defaultValue)
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60
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61 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (self.inputFileName), self.verbosity)
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62 for transcript in transcriptParser.getIterator():
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63 transcriptSize = transcript.getSize()
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64 expectedSize = transcriptSize + 2 * self.distance
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65 transcript.extendStart(self.distance)
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66 transcript.extendEnd(self.distance)
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67 theseValues = transcript.extractWigData(wigParser)
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68
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69 if len(self.strandNames) == 1:
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70 theseValues = {1: theseValues}
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71 for strand in self.strandNames:
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72 if len(theseValues[strand]) < expectedSize:
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73 theseValues[strand] = [self.defaultValue] * (expectedSize - len(theseValues[strand])) + theseValues[strand]
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74 if len(theseValues[strand]) != expectedSize:
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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))
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76 fivePValues = theseValues[strand][: self.distance]
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77 nbValues = [0.0] * (self.nbPoints)
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78 transcriptValues = [0.0] * (self.nbPoints)
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79 for i in range(self.distance, len(theseValues[strand]) - self.distance):
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80 startJ = self._iToJ(i, transcriptSize)
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81 endJ = max(startJ+1, self._iToJ(i+1, transcriptSize))
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82 for j in range(startJ, endJ):
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83 transcriptValues[j] += theseValues[strand][i]
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84 nbValues[j] += 1
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85 threePValues = theseValues[strand][-self.distance: ]
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86 values = fivePValues + [self.defaultValue if nbValue == 0 else transcriptValue / nbValue for transcriptValue, nbValue in zip(transcriptValues, nbValues)] + threePValues
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87 for i, value in enumerate(values):
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88 self.values[strand][i] += value
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89 progress.inc()
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90 progress.done()
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91
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92 for strand in self.strandNames:
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93 if strand == 0:
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94 strand = 1
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95 for i in range(self.nbPoints + 2 * self.distance):
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96 self.values[strand][i] /= transcriptParser.getNbTranscripts() * strand
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97
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98
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99 def smoothen(self):
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100 if self.smoothenForce == None:
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101 return
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102 for strand in self.strandNames:
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103 averageValues = {}
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104 for center in range(self.distance, self.distance + self.nbPoints):
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105 sum = 0.0
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106 nbValues = 0.0
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107 for i in range(center - self.smoothenForce + 1, center + self.smoothenForce):
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108 if i > self.distance and i < self.distance + self.nbPoints:
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109 nbValues += 1
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110 sum += self.values[strand][i]
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111 averageValues[center] = sum / nbValues
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112 for position in range(self.distance, self.distance + self.nbPoints):
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113 self.values[strand][position] = averageValues[position]
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114
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115
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116 def plot(self):
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117 plotter = RPlotter(self.outputFileName, self.verbosity)
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118 for strand in self.strandNames:
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119 plotter.addLine(self.values[strand])
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120 if self.log:
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121 plotter.setLog("y")
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122 plotter.setAxisLabel("x", {0: -self.distance, self.distance: "start", self.distance+self.nbPoints-1: "end", 2*self.distance+self.nbPoints-1: self.distance})
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123 plotter.plot()
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124
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125
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126
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127 if __name__ == "__main__":
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128
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129 # parse command line
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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]"
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131
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132 parser = OptionParser(description = description)
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133 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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134 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
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135 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
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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]")
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137 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="distance around genomic coordinates [compulsory] [format: int] [default: 0]")
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138 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
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139 parser.add_option("-m", "--smoothen", dest="smoothen", action="store", default=None, type="int", help="smoothen the curve [format: int] [default: None]")
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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]")
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141 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
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142 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
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143 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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144 (options, args) = parser.parse_args()
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145
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146 wigProfile = GetWigProfile(options.verbosity)
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147 wigProfile.strands = options.strands
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148 wigProfile.inputFileName = options.inputFileName
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149 wigProfile.inputFormat = options.inputFormat
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150 wigProfile.wig = options.wig
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151 wigProfile.nbPoints = options.nbPoints
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152 wigProfile.distance = options.distance
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153 wigProfile.smoothenForce = options.smoothen
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154 wigProfile.defaultValue = options.defaultValue
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155 wigProfile.outputFileName = options.outputFileName
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156 wigProfile.log = options.log
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157
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158 wigProfile.readTranscripts()
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159 wigProfile.smoothen()
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160 wigProfile.plot()