6
+ − 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 """Get the distance between the transcripts of two lists"""
+ − 32
+ − 33 import os
+ − 34 import sys
+ − 35 from optparse import OptionParser
+ − 36 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 40
+ − 41 class GetDistance(object):
+ − 42
+ − 43 def __init__(self, verbosity = 0):
+ − 44 self.verbosity = verbosity
+ − 45 self.writer = None
+ − 46 self.spearman = False
+ − 47 self.tlc = TranscriptListsComparator(None, self.verbosity)
+ − 48 self.strands = (0, )
+ − 49 self.buckets = None
+ − 50 self.title = ""
+ − 51 self.xMin = None
+ − 52 self.xMax = None
+ − 53 self.proportion = False
+ − 54 self.outputFileName = None
+ − 55 self.keep = False
+ − 56
+ − 57 def __del__(self):
+ − 58 pass
+ − 59
+ − 60 def setQueryFile(self, fileName, format):
+ − 61 self.transcriptContainer1 = TranscriptContainer(fileName, format, self.verbosity)
+ − 62
+ − 63 def setReferenceFile(self, fileName, format):
+ − 64 self.transcriptContainer2 = TranscriptContainer(fileName, format, self.verbosity)
+ − 65
+ − 66 def setOutputFile(self, fileName):
+ − 67 self.outputFileName = fileName
+ − 68
+ − 69 def setOutputTranscriptFile(self, fileName):
+ − 70 if fileName != None:
+ − 71 self.writer = Gff3Writer(fileName, self.verbosity)
+ − 72
+ − 73 def restrictQueryToStart(self, number):
+ − 74 self.tlc.restrictToStart(self.tlc.QUERY, number)
+ − 75
+ − 76 def restrictReferenceToStart(self, number):
+ − 77 self.tlc.restrictToStart(self.tlc.REFERENCE, number)
+ − 78
+ − 79 def restrictQueryToEnd(self, number):
+ − 80 self.tlc.restrictToEnd(self.tlc.QUERY, number)
+ − 81
+ − 82 def restrictReferenceToEnd(self, number):
+ − 83 self.tlc.restrictToEnd(self.tlc.REFERENCE, number)
+ − 84
+ − 85 def setAbsolute(self, boolean):
+ − 86 self.tlc.setAbsolute(boolean)
+ − 87
+ − 88 def setProportion(self, boolean):
+ − 89 self.proportion = boolean
+ − 90
+ − 91 def setColinear(self, boolean):
+ − 92 self.tlc.getColinearOnly(boolean)
+ − 93
+ − 94 def setAntisense(self, boolean):
+ − 95 self.tlc.getAntisenseOnly(boolean)
+ − 96
+ − 97 def setDistances(self, minDistance, maxDistance):
+ − 98 self.tlc.setMinDistance(minDistance)
+ − 99 self.tlc.setMaxDistance(maxDistance)
+ − 100
+ − 101 def setStrands(self, boolean):
+ − 102 self.tlc.setStrandedDistance(boolean)
+ − 103 if boolean:
+ − 104 self.strands = (-1, 1)
+ − 105
+ − 106 def setUpstream(self, number):
+ − 107 self.tlc.setUpstream(self.tlc.REFERENCE, number)
+ − 108
+ − 109 def setDownstream(self, number):
+ − 110 self.tlc.setDownstream(self.tlc.REFERENCE, number)
+ − 111
+ − 112 def setBuckets(self, number):
+ − 113 self.buckets = number
+ − 114
+ − 115 def setTitle(self, title):
+ − 116 self.title = title
+ − 117
+ − 118 def setXValues(self, xMin, xMax):
+ − 119 self.xMin, self.xMax = xMin, xMax
+ − 120
+ − 121 def keepTmpValues(self, boolean):
+ − 122 self.keep = boolean
+ − 123
+ − 124 def getSpearman(self, boolean):
+ − 125 self.spearman = True
+ − 126
+ − 127 def compare(self):
+ − 128 self.tlc.setInputTranscriptContainer(self.tlc.QUERY, self.transcriptContainer1)
+ − 129 self.tlc.setInputTranscriptContainer(self.tlc.REFERENCE, self.transcriptContainer2)
+ − 130 self.tlc.setOutputWriter(self.writer)
+ − 131 self.distances = self.tlc.compareTranscriptListDistance()
+ − 132
+ − 133 def checkEmptyDistances(self):
+ − 134 return (sum([len(self.distances[strand].keys()) for strand in self.strands]) == 0)
+ − 135
+ − 136 def setPlotterMinusStrand(self):
+ − 137 if -1 in self.strands:
+ − 138 for x, y in self.distances[-1].iteritems():
+ − 139 self.distances[-1][x] = -y
+ − 140
+ − 141 def setPlotterProportion(self):
+ − 142 if not self.proportion:
+ − 143 return
+ − 144 self.nbElements = sum([abs(sum(self.distances[strand].values())) for strand in self.strands])
+ − 145 for strand in self.strands:
+ − 146 self.distances[strand] = dict([(distance, float(nb) / self.nbElements * 100) for distance, nb in self.distances[strand].iteritems()])
+ − 147
+ − 148 def setPlotter(self):
+ − 149 self.plotter = RPlotter(self.outputFileName, self.verbosity, self.keep)
+ − 150 if self.buckets != None:
+ − 151 self.plotter.setBarplot(True)
+ − 152 self.plotter.setFill(0)
+ − 153 self.plotter.setXLabel("distance")
+ − 154 self.plotter.setYLabel("# elements")
+ − 155 if self.proportion:
+ − 156 self.plotter.setYLabel("%% elements (%d in toto)" % (self.nbElements))
+ − 157 self.plotter.setBuckets(self.buckets)
+ − 158 self.plotter.setMinimumX(self.xMin)
+ − 159 self.plotter.setMaximumX(self.xMax)
+ − 160 self.plotter.setTitle(self.title)
+ − 161
+ − 162 def plot(self):
+ − 163 if len(self.strands) == 1:
+ − 164 self.distances = {0: self.distances}
+ − 165 if self.checkEmptyDistances():
+ − 166 print "No output."
+ − 167 sys.exit()
+ − 168 self.setPlotterMinusStrand()
+ − 169 self.setPlotterProportion()
+ − 170 if self.outputFileName == None:
+ − 171 return
+ − 172 self.setPlotter()
+ − 173 for strand in self.strands:
+ − 174 self.plotter.addLine(self.distances[strand])
+ − 175 self.plotter.plot()
+ − 176
+ − 177 def printSpearman(self):
+ − 178 if self.spearman:
+ − 179 print "Spearman's rho: %.5f" % (self.plotter.getSpearmanRho())
+ − 180
+ − 181 def run(self):
+ − 182 self.compare()
+ − 183 self.plot()
+ − 184 self.printSpearman()
+ − 185
+ − 186 if __name__ == "__main__":
+ − 187
+ − 188 # parse command line
+ − 189 description = "Get Distance v1.0.3: Compute the distance of a set of transcript with respect to a reference set. [Category: Visualization]"
+ − 190
+ − 191 parser = OptionParser(description = description)
+ − 192 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+ − 193 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+ − 194 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+ − 195 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+ − 196 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="plot output file [format: output file in PNG format]")
+ − 197 parser.add_option("-O", "--outputDistances", dest="outputDistances", action="store", default=None, type="string", help="output file containing the distance for each element of the query [format: output file in GFF3 format] [default: None]")
+ − 198 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="only consider features on the same strand [format: bool] [default: false]")
+ − 199 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="only consider features on the opposite strand [format: bool] [default: false]")
+ − 200 parser.add_option("-b", "--absolute", dest="absolute", action="store_true", default=False, help="give the absolute value of the distance [format: bool] [default: false]")
+ − 201 parser.add_option("-p", "--proportion", dest="proportion", action="store_true", default=False, help="give the proportion on the y-axis instead of the number of distances [format: bool] [default: false]")
+ − 202 parser.add_option("-s", "--start1", dest="start1", action="store", default=None, type="int", help="only consider the n first 5' nucleotides for list 1 [format: int]")
+ − 203 parser.add_option("-S", "--start2", dest="start2", action="store", default=None, type="int", help="only consider the n first 5' nucleotides for list 2 [format: int]")
+ − 204 parser.add_option("-e", "--end1", dest="end1", action="store", default=None, type="int", help="only consider the n last 3' nucleotides for list 1 [format: int]")
+ − 205 parser.add_option("-E", "--end2", dest="end2", action="store", default=None, type="int", help="only consider the n last 3' nucleotides for list 2 [format: int]")
+ − 206 parser.add_option("-m", "--minDistance", dest="minDistance", action="store", default=None, type="int", help="minimum distance considered between two transcripts [format: int] [default: None]")
+ − 207 parser.add_option("-M", "--maxDistance", dest="maxDistance", action="store", default=1000, type="int", help="maximum distance considered between two transcripts [format: int] [default: 1000]")
+ − 208 parser.add_option("-5", "--fivePrime", dest="fivePrime", action="store_true", default=False, help="consider the elements from list 1 which are upstream of elements of list 2 [format: bool] [default: False]")
+ − 209 parser.add_option("-3", "--threePrime", dest="threePrime", action="store_true", default=False, help="consider the elements from list 1 which are downstream of elements of list 2 [format: bool] [default: False]")
+ − 210 parser.add_option("-u", "--buckets", dest="buckets", action="store", default=None, type="int", help="plot histogram instead of line plot with given interval size [format: int] [default: None]")
+ − 211 parser.add_option("-2", "--2strands", dest="twoStrands", action="store_true", default=False, help="plot the distributions of each strand separately [format: bool] [default: False]")
+ − 212 parser.add_option("-r", "--spearman", dest="spearman", action="store_true", default=False, help="compute Spearman rho [format: bool] [default: False]")
+ − 213 parser.add_option("-x", "--xMin", dest="xMin", action="store", default=None, type="int", help="minimum value on the x-axis to plot [format: int] [default: None]")
+ − 214 parser.add_option("-X", "--xMax", dest="xMax", action="store", default=None, type="int", help="maximum value on the x-axis to plot [format: int] [default: None]")
+ − 215 parser.add_option("-t", "--title", dest="title", action="store", default=None, type="string", help="title for the graph [format: int] [default: None]")
+ − 216 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 217 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: bool]")
+ − 218 (options, args) = parser.parse_args()
+ − 219
+ − 220 gd = GetDistance(options.verbosity)
+ − 221 gd.setQueryFile(options.inputFileName1, options.format1)
+ − 222 gd.setReferenceFile(options.inputFileName2, options.format2)
+ − 223 gd.setOutputFile(options.outputFileName)
+ − 224 gd.setOutputTranscriptFile(options.outputDistances)
+ − 225 gd.setColinear(options.colinear)
+ − 226 gd.setAntisense(options.antisense)
+ − 227 gd.setAbsolute(options.absolute)
+ − 228 gd.setProportion(options.proportion)
+ − 229 gd.restrictQueryToStart(options.start1)
+ − 230 gd.restrictReferenceToStart(options.start2)
+ − 231 gd.restrictQueryToEnd(options.end1)
+ − 232 gd.restrictReferenceToEnd(options.end2)
+ − 233 gd.setDistances(options.minDistance, options.maxDistance)
+ − 234 gd.setUpstream(options.fivePrime)
+ − 235 gd.setDownstream(options.threePrime)
+ − 236 gd.setStrands(options.twoStrands)
+ − 237 gd.setBuckets(options.buckets)
+ − 238 gd.setTitle(options.title)
+ − 239 gd.setXValues(options.xMin, options.xMax)
+ − 240 gd.keepTmpValues(options.keep)
+ − 241 gd.run()
