6
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2012
+ − 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 import os
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.ParserChooser import ParserChooser
+ − 34 from commons.core.parsing.FastaParser import FastaParser
+ − 35 from SMART.Java.Python.structure.Transcript import Transcript
+ − 36 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 37 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 38 from SMART.Java.Python.misc.MultipleRPlotter import MultipleRPlotter
+ − 39 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 40 from SMART.Java.Python.misc.Progress import Progress
+ − 41
+ − 42 TWOSTRANDS = {True: [1, -1], False: [0]}
+ − 43 STRANDTOSTR = {1: "(+)", -1: "(-)", 0: ""}
+ − 44
+ − 45 class GetDistribution(object):
+ − 46
+ − 47 def __init__(self, verbosity):
+ − 48 self.verbosity = verbosity
+ − 49 self.sizes = None
+ − 50 self.twoStrands = False
+ − 51 self.start = 1
+ − 52 self.names = ["nbElements"]
+ − 53 self.average = False
+ − 54 self.nbValues = {}
+ − 55 self.height = 300
+ − 56 self.width = 600
+ − 57 self.colors = None
+ − 58 self.gffFileName = None
+ − 59 self.csvFileName = None
+ − 60 self.yMin = None
+ − 61 self.yMax = None
+ − 62 self.chromosome = None
+ − 63 self.merge = False
+ − 64 self.nbTranscripts = None
+ − 65
+ − 66 def setInputFile(self, fileName, format):
+ − 67 chooser = ParserChooser(self.verbosity)
+ − 68 chooser.findFormat(format)
+ − 69 self.parser = chooser.getParser(fileName)
+ − 70
+ − 71 def setReferenceFile(self, fileName):
+ − 72 if fileName == None:
+ − 73 return
+ − 74 fastaParser = FastaParser(fileName, self.verbosity)
+ − 75 self.chromosomes = fastaParser.getRegions()
+ − 76 self.sizes = dict([region, fastaParser.getSizeOfRegion(region)] for region in self.chromosomes)
+ − 77 self.maxSize = max(self.sizes.values())
+ − 78
+ − 79 def setRegion(self, chromosome, start, end):
+ − 80 if chromosome == None:
+ − 81 return
+ − 82 self.maxSize = options.end
+ − 83 self.sizes = {chromosome: end}
+ − 84 self.chromosomes = [chromosome]
+ − 85 self.chromosome = chromosome
+ − 86 self.start = start
+ − 87 self.end = end
+ − 88
+ − 89 def setOutputFile(self, fileName):
+ − 90 self.outputFileName = fileName
+ − 91
+ − 92 def setNbBins(self, nbBins):
+ − 93 self.nbBins = nbBins
+ − 94
+ − 95 def set2Strands(self, twoStrands):
+ − 96 self.twoStrands = twoStrands
+ − 97
+ − 98 def setNames(self, names):
+ − 99 self.names = names
+ − 100
+ − 101 def setAverage(self, average):
+ − 102 self.average = average
+ − 103
+ − 104 def setNormalization(self, normalization):
+ − 105 self.normalization = normalization
+ − 106
+ − 107 def setImageSize(self, height, width):
+ − 108 self.height = height
+ − 109 self.width = width
+ − 110
+ − 111 def setYLimits(self, yMin, yMax):
+ − 112 self.yMin = yMin
+ − 113 self.yMax = yMax
+ − 114
+ − 115 def setColors(self, colors):
+ − 116 self.colors = colors
+ − 117
+ − 118 def writeGff(self, fileName):
+ − 119 self.gffFileName = fileName
+ − 120
+ − 121 def writeCsv(self, fileName):
+ − 122 self.csvFileName = fileName
+ − 123
+ − 124 def mergePlots(self, merge):
+ − 125 self.merge = merge
+ − 126
+ − 127 def _estimateSizes(self):
+ − 128 progress = UnlimitedProgress(10000, "Reading input for chromosome size estimate", self.verbosity)
+ − 129 self.sizes = {}
+ − 130 for self.nbTranscripts, transcript in enumerate(self.parser.getIterator()):
+ − 131 chromosome = transcript.getChromosome()
+ − 132 start = transcript.getStart()
+ − 133 self.sizes[chromosome] = max(start, self.sizes.get(chromosome, 0))
+ − 134 progress.inc()
+ − 135 progress.done()
+ − 136
+ − 137 def _computeSliceSize(self):
+ − 138 if self.nbBins == 0:
+ − 139 return
+ − 140 tmp1 = int(max(self.sizes.values()) / float(self.nbBins))
+ − 141 tmp2 = 10 ** (len("%d" % (tmp1))-2)
+ − 142 self.sliceSize = max(1, int((tmp1 / tmp2) * tmp2))
+ − 143 if self.verbosity > 0:
+ − 144 print "choosing bin size of %d" % (self.sliceSize)
+ − 145
+ − 146 def _initBins(self):
+ − 147 self.bins = {}
+ − 148 for chromosome in self.sizes:
+ − 149 self.bins[chromosome] = {}
+ − 150 for name in self.names:
+ − 151 self.bins[chromosome][name] = {}
+ − 152 for strand in TWOSTRANDS[self.twoStrands]:
+ − 153 if self.nbBins == 0:
+ − 154 self.bins[chromosome][name][strand] = {}
+ − 155 else:
+ − 156 self.bins[chromosome][name][strand] = dict([(i * self.sliceSize + 1, 0.0) for i in range(self.start / self.sliceSize, self.sizes[chromosome] / self.sliceSize + 1)])
+ − 157
+ − 158 def _populateBins(self):
+ − 159 if self.nbTranscripts == None:
+ − 160 progress = UnlimitedProgress(10000, "Counting data", self.verbosity)
+ − 161 else:
+ − 162 progress = Progress(self.nbTranscripts, "Counting data", self.verbosity)
+ − 163 for transcript in self.parser.getIterator():
+ − 164 if transcript.__class__.__name__ == "Mapping":
+ − 165 transcript = transcript.getTranscript()
+ − 166 progress.inc()
+ − 167 chromosome = transcript.getChromosome()
+ − 168 start = transcript.getStart()
+ − 169 if self.chromosome and (chromosome != self.chromosome or start < self.start or start > self.end):
+ − 170 continue
+ − 171 strand = transcript.getDirection() if self.twoStrands else 0
+ − 172 if self.nbBins != 0:
+ − 173 bin = (start / self.sliceSize) * self.sliceSize + 1
+ − 174 else:
+ − 175 bin = start
+ − 176 for name in self.names:
+ − 177 value = float(transcript.tags.get(name, 1))
+ − 178 self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + value
+ − 179 self.nbValues[name] = self.nbValues.get(name, 0) + value
+ − 180 progress.done()
+ − 181
+ − 182 def _normalize(self):
+ − 183 average = float(sum(self.nbValues)) / len(self.nbValues.keys())
+ − 184 factors = dict([name, float(average) / self.nbValues[name]] for name in self.nbValues)
+ − 185 for chromosome in self.bins:
+ − 186 for name in self.bins[chromosome]:
+ − 187 for strand in self.bins[chromosome][name]:
+ − 188 for bin in self.bins[chromosome][name][strand]:
+ − 189 self.bins[chromosome][name][strand][bin] *= factors[name]
+ − 190
+ − 191 def _computeAverage(self):
+ − 192 for chromosome in self.bins:
+ − 193 for name in self.bins[chromosome]:
+ − 194 for strand in self.bins[chromosome][name]:
+ − 195 for bin in self.bins[chromosome][name][strand]:
+ − 196 self.bins[chromosome][name][strand][bin] = float(self.bins[chromosome][name][strand][bin]) / self.sliceSize
+ − 197
+ − 198 def _getPlotter(self, chromosome):
+ − 199 plot = RPlotter("%s_%s.png" % (os.path.splitext(self.outputFileName)[0], chromosome), self.verbosity)
+ − 200 plot.setImageSize(self.width, self.height)
+ − 201 if self.sizes[chromosome] <= 1000:
+ − 202 unit = "nt."
+ − 203 ratio = 1.0
+ − 204 elif self.sizes[chromosome] <= 1000000:
+ − 205 unit = "kb"
+ − 206 ratio = 1000.0
+ − 207 else:
+ − 208 unit = "Mb"
+ − 209 ratio = 1000000.0
+ − 210 if self.yMin != None:
+ − 211 plot.setMinimumY(self.yMin)
+ − 212 if self.yMax != None:
+ − 213 plot.setMaximumY(self.yMax)
+ − 214 plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
+ − 215 plot.setLegend(True)
+ − 216 for i, name in enumerate(self.bins[chromosome]):
+ − 217 for strand in self.bins[chromosome][name]:
+ − 218 fullName = "%s %s" % (name.replace("_", " ")[:6], STRANDTOSTR[strand])
+ − 219 factor = 1 if strand == 0 else strand
+ − 220 correctedLine = dict([(key / ratio, value * factor) for key, value in self.bins[chromosome][name][strand].iteritems()])
+ − 221 plot.addLine(correctedLine, fullName, self.colors[i] if self.colors else None)
+ − 222 return plot
+ − 223
+ − 224 def _plot(self):
+ − 225 if self.merge:
+ − 226 multiplePlot = MultipleRPlotter(self.outputFileName, self.verbosity)
+ − 227 multiplePlot.setImageSize(self.width, self.height * len(self.bins.keys()))
+ − 228 progress = Progress(len(self.bins.keys()), "Plotting", options.verbosity)
+ − 229 for chromosome in sorted(self.bins.keys()):
+ − 230 plot = self._getPlotter(chromosome)
+ − 231 if self.merge:
+ − 232 multiplePlot.addPlot(plot)
+ − 233 else:
+ − 234 plot.plot()
+ − 235 progress.inc()
+ − 236 if self.merge:
+ − 237 multiplePlot.plot()
+ − 238 progress.done()
+ − 239
+ − 240 def _writeCsv(self):
+ − 241 if self.verbosity > 1:
+ − 242 print "Writing CSV file..."
+ − 243 csvHandle = open(self.csvFileName, "w")
+ − 244 csvHandle.write("chromosome;tag;strand")
+ − 245 if self.nbBins != 0:
+ − 246 xValues = range(self.start / self.sliceSize, max(self.sizes.values()) / self.sliceSize + 1)
+ − 247 for value in xValues:
+ − 248 csvHandle.write(";%d-%d" % (value * self.sliceSize + 1, (value+1) * self.sliceSize))
+ − 249 csvHandle.write("\n")
+ − 250 else:
+ − 251 xValues = []
+ − 252 for chromosome in self.bins:
+ − 253 for name in self.bins[chromosome]:
+ − 254 for strand in self.bins[chromosome][name]:
+ − 255 for bin in self.bins[chromosome][name][strand]:
+ − 256 xValues.extend(self.bins[chromosome][name][strand].keys())
+ − 257 xValues = sorted(list(set(xValues)))
+ − 258 for value in xValues:
+ − 259 csvHandle.write(";%d" % (value))
+ − 260 csvHandle.write("\n")
+ − 261 for chromosome in self.bins:
+ − 262 csvHandle.write("%s" % (chromosome))
+ − 263 for name in self.bins[chromosome]:
+ − 264 csvHandle.write(";%s" % (name))
+ − 265 for strand in self.bins[chromosome][name]:
+ − 266 csvHandle.write(";%s" % (STRANDTOSTR[strand]))
+ − 267 for bin in xValues:
+ − 268 csvHandle.write(";%.2f" % (self.bins[chromosome][name][strand].get(bin, 0)))
+ − 269 csvHandle.write("\n")
+ − 270 csvHandle.write(";")
+ − 271 csvHandle.write(";")
+ − 272 csvHandle.close()
+ − 273 if self.verbosity > 1:
+ − 274 print "...done"
+ − 275
+ − 276 def _writeGff(self):
+ − 277 if self.verbosity > 1:
+ − 278 print "Writing GFF file..."
+ − 279 writer = Gff3Writer(self.gffFileName, self.verbosity)
+ − 280 cpt = 1
+ − 281 for chromosome in self.bins:
+ − 282 for name in self.bins[chromosome]:
+ − 283 for strand in self.bins[chromosome][name]:
+ − 284 for bin in self.bins[chromosome][name][strand]:
+ − 285 transcript = Transcript()
+ − 286 transcript.setChromosome(chromosome)
+ − 287 transcript.setStart(bin)
+ − 288 if self.nbBins > 0:
+ − 289 transcript.setEnd(bin + self.sliceSize)
+ − 290 else:
+ − 291 transcript.setEnd(start)
+ − 292 transcript.setDirection(1 if strand == 0 else strand)
+ − 293 transcript.setTagValue("ID", "region%d" % (cpt))
+ − 294 cpt += 1
+ − 295 writer.write()
+ − 296 if self.verbosity > 1:
+ − 297 print "...done"
+ − 298
+ − 299 def run(self):
+ − 300 if self.sizes == None:
+ − 301 self._estimateSizes()
+ − 302 self._computeSliceSize()
+ − 303 self._initBins()
+ − 304 self._populateBins()
+ − 305 if self.normalization:
+ − 306 self._normalize()
+ − 307 if self.average:
+ − 308 self._computeAverage()
+ − 309 self._plot()
+ − 310 if self.csvFileName != None:
+ − 311 self._writeCsv()
+ − 312 if self.gffFileName != None:
+ − 313 self._writeGff()
+ − 314
+ − 315
+ − 316 if __name__ == "__main__":
+ − 317
+ − 318 description = "Get Distribution v1.0.2: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
+ − 319
+ − 320 parser = OptionParser(description = description)
+ − 321 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 322 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
+ − 323 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 324 parser.add_option("-r", "--reference", dest="referenceFileName", action="store", default=None, type="string", help="file containing the genome [format: file in FASTA format]")
+ − 325 parser.add_option("-b", "--nbBins", dest="nbBins", action="store", default=1000, type="int", help="number of bins [default: 1000] [format: int]")
+ − 326 parser.add_option("-2", "--bothStrands", dest="bothStrands", action="store_true", default=False, help="plot one curve per strand [format: bool] [default: false]")
+ − 327 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="plot only a chromosome [format: string]")
+ − 328 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start from a given region [format: int]")
+ − 329 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end from a given region [format: int]")
+ − 330 parser.add_option("-y", "--yMin", dest="yMin", action="store", default=None, type="int", help="minimum value on the y-axis to plot [format: int]")
+ − 331 parser.add_option("-Y", "--yMax", dest="yMax", action="store", default=None, type="int", help="maximum value on the y-axis to plot [format: int]")
+ − 332 parser.add_option("-x", "--csv", dest="csv", action="store", default=None, help="write a .csv file [format: output file in CSV format] [default: None]")
+ − 333 parser.add_option("-g", "--gff", dest="gff", action="store", default=None, help="also write GFF3 file [format: output file in GFF format] [default: None]")
+ − 334 parser.add_option("-H", "--height", dest="height", action="store", default=300, type="int", help="height of the graphics [format: int] [default: 300]")
+ − 335 parser.add_option("-W", "--width", dest="width", action="store", default=600, type="int", help="width of the graphics [format: int] [default: 1000]")
+ − 336 parser.add_option("-a", "--average", dest="average", action="store_true", default=False, help="plot average (instead of sum) [default: false] [format: boolean]")
+ − 337 parser.add_option("-n", "--names", dest="names", action="store", default="nbElements", type="string", help="name for the tags (separated by commas and no space) [default: None] [format: string]")
+ − 338 parser.add_option("-l", "--color", dest="colors", action="store", default=None, type="string", help="color of the lines (separated by commas and no space) [format: string]")
+ − 339 parser.add_option("-z", "--normalize", dest="normalize", action="store_true", default=False, help="normalize data (when panels are different) [format: bool] [default: false]")
+ − 340 parser.add_option("-m", "--merge", dest="mergePlots", action="store_true", default=False, help="merge all plots in one figure [format: bool] [default: false]")
+ − 341 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
+ − 342 (options, args) = parser.parse_args()
+ − 343
+ − 344 gt = GetDistribution(options.verbosity)
+ − 345 gt.setInputFile(options.inputFileName, options.format)
+ − 346 gt.setOutputFile(options.outputFileName)
+ − 347 gt.setReferenceFile(options.referenceFileName)
+ − 348 gt.setNbBins(int(options.nbBins))
+ − 349 gt.set2Strands(options.bothStrands)
+ − 350 gt.setRegion(options.chromosome, options.start, options.end)
+ − 351 gt.setNormalization(options.normalize)
+ − 352 gt.setAverage(options.average)
+ − 353 gt.setYLimits(options.yMin, options.yMax)
+ − 354 gt.writeCsv(options.csv)
+ − 355 gt.writeGff(options.gff)
+ − 356 gt.setImageSize(options.height, options.width)
+ − 357 gt.setNames(options.names.split(","))
+ − 358 gt.setColors(None if options.colors == None else options.colors.split(","))
+ − 359 gt.setNormalization(options.normalize)
+ − 360 gt.mergePlots(options.mergePlots)
+ − 361 gt.run()
+ − 362
