36
+ − 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):
46
+ − 48 self.verbosity = verbosity
+ − 49 self.sizes = None
+ − 50 self.nbBins = None
+ − 51 self.sliceSize = None
+ − 52 self.twoStrands = False
+ − 53 self.start = 1
+ − 54 self.names = ["nbElements"]
+ − 55 self.average = False
+ − 56 self.nbValues = {}
+ − 57 self.height = 300
+ − 58 self.width = 600
+ − 59 self.dots = False
+ − 60 self.colors = None
+ − 61 self.gffFileName = None
+ − 62 self.csvFileName = None
+ − 63 self.yMin = None
+ − 64 self.yMax = None
+ − 65 self.chromosome = None
+ − 66 self.merge = False
+ − 67 self.nbTranscripts = None
+ − 68 self.factors = None
+ − 69 self.thicknessCurve = 1
+ − 70 self.sizePoliceLegend = 1.5
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+ − 71
46
+ − 72 def setInputFiles(self, fileNames, format):
+ − 73 self.fileNames = fileNames
+ − 74 self.format = format
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+ − 75
+ − 76 def setReferenceFile(self, fileName):
+ − 77 if fileName == None:
+ − 78 return
+ − 79 fastaParser = FastaParser(fileName, self.verbosity)
+ − 80 self.chromosomes = fastaParser.getRegions()
+ − 81 self.sizes = dict([region, fastaParser.getSizeOfRegion(region)] for region in self.chromosomes)
+ − 82 self.maxSize = max(self.sizes.values())
+ − 83
+ − 84 def setRegion(self, chromosome, start, end):
46
+ − 85 if chromosome == None or start == None or end == None:
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+ − 86 return
+ − 87 self.maxSize = options.end
+ − 88 self.sizes = {chromosome: end}
+ − 89 self.chromosomes = [chromosome]
+ − 90 self.chromosome = chromosome
+ − 91 self.start = start
+ − 92 self.end = end
+ − 93
+ − 94 def setOutputFile(self, fileName):
+ − 95 self.outputFileName = fileName
+ − 96
+ − 97 def setNbBins(self, nbBins):
46
+ − 98 if nbBins != None:
+ − 99 self.nbBins = int(nbBins)
+ − 100
+ − 101 def setBinSize(self, binSize):
+ − 102 if binSize != None:
+ − 103 self.sliceSize = int(binSize)
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+ − 104
+ − 105 def set2Strands(self, twoStrands):
+ − 106 self.twoStrands = twoStrands
+ − 107
+ − 108 def setNames(self, names):
+ − 109 self.names = names
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+ − 110 if len(self.names) == 1 and len(self.fileNames) > 1:
+ − 111 self.names = ["file %d" % (i+1) for i in range(len(self.fileNames))]
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+ − 112
+ − 113 def setAverage(self, average):
+ − 114 self.average = average
+ − 115
+ − 116 def setNormalization(self, normalization):
+ − 117 self.normalization = normalization
+ − 118
46
+ − 119 def setNormalizationFactors(self, factors):
+ − 120 self.factors = dict([name, 1.0] for name in self.names) if factors == None else dict(zip(self.names, factors))
+ − 121
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+ − 122 def setImageSize(self, height, width):
+ − 123 self.height = height
+ − 124 self.width = width
+ − 125
46
+ − 126 def setDots(self, dots):
+ − 127 self.dots = dots
+ − 128
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+ − 129 def setYLimits(self, yMin, yMax):
+ − 130 self.yMin = yMin
+ − 131 self.yMax = yMax
+ − 132
+ − 133 def setColors(self, colors):
+ − 134 self.colors = colors
+ − 135
+ − 136 def writeGff(self, fileName):
+ − 137 self.gffFileName = fileName
+ − 138
+ − 139 def writeCsv(self, fileName):
+ − 140 self.csvFileName = fileName
+ − 141
+ − 142 def mergePlots(self, merge):
+ − 143 self.merge = merge
+ − 144
46
+ − 145 def setThicknessCurve(self, thickness) :
+ − 146 self.thickness = thickness
+ − 147
+ − 148 def setSizePoliceLegend(self, sizePoliceLegend):
+ − 149 self.sizePoliceLegend = sizePoliceLegend
+ − 150
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+ − 151 def _estimateSizes(self):
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+ − 152 self.sizes = {}
+ − 153 self.nbTranscripts = {}
+ − 154 for fileName in self.fileNames:
+ − 155 progress = UnlimitedProgress(10000, "Reading %s for chromosome size estimate" % (fileName), self.verbosity)
+ − 156 parserChooser = ParserChooser(self.verbosity)
+ − 157 parserChooser.findFormat(self.format)
+ − 158 parser = parserChooser.getParser(fileName)
+ − 159 for nbTranscripts, transcript in enumerate(parser.getIterator()):
+ − 160 if transcript.__class__.__name__ == "Mapping":
+ − 161 transcript = transcript.getTranscript()
+ − 162 chromosome = transcript.getChromosome()
+ − 163 start = transcript.getStart()
+ − 164 self.sizes[chromosome] = max(start, self.sizes.get(chromosome, 0))
+ − 165 progress.inc()
+ − 166 progress.done()
+ − 167 self.nbTranscripts[fileName] = nbTranscripts
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+ − 168
+ − 169 def _computeSliceSize(self):
+ − 170 if self.nbBins == 0:
+ − 171 return
+ − 172 tmp1 = int(max(self.sizes.values()) / float(self.nbBins))
+ − 173 tmp2 = 10 ** (len("%d" % (tmp1))-2)
+ − 174 self.sliceSize = max(1, int((tmp1 / tmp2) * tmp2))
+ − 175 if self.verbosity > 0:
+ − 176 print "choosing bin size of %d" % (self.sliceSize)
+ − 177
+ − 178 def _initBins(self):
+ − 179 self.bins = {}
+ − 180 for chromosome in self.sizes:
+ − 181 self.bins[chromosome] = {}
+ − 182 for name in self.names:
+ − 183 self.bins[chromosome][name] = {}
+ − 184 for strand in TWOSTRANDS[self.twoStrands]:
+ − 185 if self.nbBins == 0:
+ − 186 self.bins[chromosome][name][strand] = {}
+ − 187 else:
+ − 188 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)])
+ − 189
+ − 190 def _populateBins(self):
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+ − 191 for id, fileName in enumerate(self.fileNames):
+ − 192 if self.nbTranscripts == None:
+ − 193 progress = UnlimitedProgress(10000, "Counting data", self.verbosity)
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+ − 194 else:
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+ − 195 progress = Progress(self.nbTranscripts[fileName], "Counting data", self.verbosity)
+ − 196 parserChooser = ParserChooser(self.verbosity)
+ − 197 parserChooser.findFormat(self.format)
+ − 198 parser = parserChooser.getParser(fileName)
+ − 199 for transcript in parser.getIterator():
+ − 200 if transcript.__class__.__name__ == "Mapping":
+ − 201 transcript = transcript.getTranscript()
+ − 202 progress.inc()
+ − 203 chromosome = transcript.getChromosome()
+ − 204 start = transcript.getStart()
+ − 205 if self.chromosome and (chromosome != self.chromosome or start < self.start or start > self.end):
+ − 206 continue
+ − 207 strand = transcript.getDirection() if self.twoStrands else 0
+ − 208 if self.nbBins != 0:
+ − 209 bin = (start / self.sliceSize) * self.sliceSize + 1
+ − 210 else:
+ − 211 bin = start
+ − 212 if len(self.fileNames) > 1:
+ − 213 nbElements = transcript.getTagValue("nbElements") if "nbElements" in transcript.getTagNames() else 1
+ − 214 name = self.names[id]
+ − 215 self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + nbElements
+ − 216 self.nbValues[name] = self.nbValues.get(name, 0) + nbElements
+ − 217 else:
+ − 218 for name in self.names:
+ − 219 value = float(transcript.tags.get(name, 1))
+ − 220 self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + value
+ − 221 self.nbValues[name] = self.nbValues.get(name, 0) + value
+ − 222 progress.done()
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+ − 223
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+ − 224 def _normalizeFactors(self):
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+ − 225 for chromosome in self.bins:
+ − 226 for name in self.bins[chromosome]:
+ − 227 for strand in self.bins[chromosome][name]:
+ − 228 for bin in self.bins[chromosome][name][strand]:
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+ − 229 self.bins[chromosome][name][strand][bin] *= self.factors[name]
+ − 230
+ − 231 def _normalize(self):
+ − 232 average = float(sum(self.nbValues.values())) / len(self.nbValues.keys())
+ − 233 self.factors = dict([name, float(average) / self.nbValues[name]] for name in self.nbValues)
+ − 234 self._normalizeFactors()
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+ − 235
+ − 236 def _computeAverage(self):
+ − 237 for chromosome in self.bins:
+ − 238 for name in self.bins[chromosome]:
+ − 239 for strand in self.bins[chromosome][name]:
+ − 240 for bin in self.bins[chromosome][name][strand]:
+ − 241 self.bins[chromosome][name][strand][bin] = float(self.bins[chromosome][name][strand][bin]) / self.sliceSize
+ − 242
+ − 243 def _getPlotter(self, chromosome):
+ − 244 plot = RPlotter("%s_%s.png" % (os.path.splitext(self.outputFileName)[0], chromosome), self.verbosity)
+ − 245 plot.setImageSize(self.width, self.height)
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+ − 246 plot.setLineWidth(self.thickness)
+ − 247 plot.setSizePoliceLegend(self.sizePoliceLegend)
+ − 248 if self.dots:
+ − 249 plot.setPoints(True)
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+ − 250 if self.sizes[chromosome] <= 1000:
+ − 251 unit = "nt."
+ − 252 ratio = 1.0
+ − 253 elif self.sizes[chromosome] <= 1000000:
+ − 254 unit = "kb"
+ − 255 ratio = 1000.0
+ − 256 else:
+ − 257 unit = "Mb"
+ − 258 ratio = 1000000.0
+ − 259 if self.yMin != None:
+ − 260 plot.setMinimumY(self.yMin)
+ − 261 if self.yMax != None:
+ − 262 plot.setMaximumY(self.yMax)
+ − 263 plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
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+ − 264 if len(self.names) > 1:
+ − 265 plot.setLegend(True, True)
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+ − 266 for i, name in enumerate(self.bins[chromosome]):
+ − 267 for strand in self.bins[chromosome][name]:
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+ − 268 #fullName = "%s %s" % (name.replace("_", " ")[:6], STRANDTOSTR[strand])
+ − 269 fullName = name.replace("_", " ")[:6]
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+ − 270 factor = 1 if strand == 0 else strand
+ − 271 correctedLine = dict([(key / ratio, value * factor) for key, value in self.bins[chromosome][name][strand].iteritems()])
+ − 272 plot.addLine(correctedLine, fullName, self.colors[i] if self.colors else None)
+ − 273 return plot
+ − 274
+ − 275 def _plot(self):
+ − 276 if self.merge:
+ − 277 multiplePlot = MultipleRPlotter(self.outputFileName, self.verbosity)
+ − 278 multiplePlot.setImageSize(self.width, self.height * len(self.bins.keys()))
+ − 279 progress = Progress(len(self.bins.keys()), "Plotting", options.verbosity)
+ − 280 for chromosome in sorted(self.bins.keys()):
+ − 281 plot = self._getPlotter(chromosome)
+ − 282 if self.merge:
+ − 283 multiplePlot.addPlot(plot)
+ − 284 else:
+ − 285 plot.plot()
+ − 286 progress.inc()
+ − 287 if self.merge:
+ − 288 multiplePlot.plot()
+ − 289 progress.done()
+ − 290
+ − 291 def _writeCsv(self):
+ − 292 if self.verbosity > 1:
+ − 293 print "Writing CSV file..."
+ − 294 csvHandle = open(self.csvFileName, "w")
+ − 295 csvHandle.write("chromosome;tag;strand")
+ − 296 if self.nbBins != 0:
+ − 297 xValues = range(self.start / self.sliceSize, max(self.sizes.values()) / self.sliceSize + 1)
+ − 298 for value in xValues:
+ − 299 csvHandle.write(";%d-%d" % (value * self.sliceSize + 1, (value+1) * self.sliceSize))
+ − 300 csvHandle.write("\n")
+ − 301 else:
+ − 302 xValues = []
+ − 303 for chromosome in self.bins:
+ − 304 for name in self.bins[chromosome]:
+ − 305 for strand in self.bins[chromosome][name]:
+ − 306 for bin in self.bins[chromosome][name][strand]:
+ − 307 xValues.extend(self.bins[chromosome][name][strand].keys())
+ − 308 xValues = sorted(list(set(xValues)))
+ − 309 for value in xValues:
+ − 310 csvHandle.write(";%d" % (value))
+ − 311 csvHandle.write("\n")
+ − 312 for chromosome in self.bins:
+ − 313 csvHandle.write("%s" % (chromosome))
+ − 314 for name in self.bins[chromosome]:
+ − 315 csvHandle.write(";%s" % (name))
+ − 316 for strand in self.bins[chromosome][name]:
+ − 317 csvHandle.write(";%s" % (STRANDTOSTR[strand]))
+ − 318 for bin in xValues:
+ − 319 csvHandle.write(";%.2f" % (self.bins[chromosome][name][strand].get(bin, 0)))
+ − 320 csvHandle.write("\n")
+ − 321 csvHandle.write(";")
+ − 322 csvHandle.write(";")
+ − 323 csvHandle.close()
+ − 324 if self.verbosity > 1:
+ − 325 print "...done"
+ − 326
+ − 327 def _writeGff(self):
+ − 328 if self.verbosity > 1:
+ − 329 print "Writing GFF file..."
+ − 330 writer = Gff3Writer(self.gffFileName, self.verbosity)
+ − 331 cpt = 1
+ − 332 for chromosome in self.bins:
+ − 333 for name in self.bins[chromosome]:
+ − 334 for strand in self.bins[chromosome][name]:
+ − 335 for bin in self.bins[chromosome][name][strand]:
+ − 336 transcript = Transcript()
+ − 337 transcript.setChromosome(chromosome)
+ − 338 transcript.setStart(bin)
+ − 339 if self.nbBins > 0:
+ − 340 transcript.setEnd(bin + self.sliceSize)
+ − 341 else:
+ − 342 transcript.setEnd(self.start)
+ − 343 transcript.setDirection(1 if strand == 0 else strand)
+ − 344 transcript.setTagValue("ID", "region%d" % (cpt))
+ − 345 cpt += 1
+ − 346 writer.write()
+ − 347 if self.verbosity > 1:
+ − 348 print "...done"
+ − 349
+ − 350 def run(self):
+ − 351 if self.sizes == None:
+ − 352 self._estimateSizes()
46
+ − 353 if self.sliceSize == None:
+ − 354 self._computeSliceSize()
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+ − 355 self._initBins()
+ − 356 self._populateBins()
+ − 357 if self.normalization:
+ − 358 self._normalize()
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+ − 359 if self.factors != None:
+ − 360 self._normalizeFactors()
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+ − 361 if self.average:
+ − 362 self._computeAverage()
+ − 363 self._plot()
+ − 364 if self.csvFileName != None:
+ − 365 self._writeCsv()
+ − 366 if self.gffFileName != None:
+ − 367 self._writeGff()
+ − 368
+ − 369
+ − 370 if __name__ == "__main__":
+ − 371
+ − 372 description = "Get Distribution v1.0.2: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
+ − 373
+ − 374 parser = OptionParser(description = description)
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+ − 375 parser.add_option("-i", "--input", dest="inputFileNames", action="store", type="string", help="input files separated by commas [compulsory] [format: string]")
+ − 376 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
+ − 377 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 378 parser.add_option("-r", "--reference", dest="referenceFileName", action="store", default=None, type="string", help="file containing the genome [format: file in FASTA format]")
+ − 379 parser.add_option("-b", "--nbBins", dest="nbBins", action="store", default=1000, type="int", help="number of bins [default: 1000] [format: int]")
+ − 380 parser.add_option("-B", "--binSize", dest="binSize", action="store", default=None, type="int", help="bin size [default: None] [format: int]")
+ − 381 parser.add_option("-2", "--bothStrands", dest="bothStrands", action="store_true", default=False, help="plot one curve per strand [format: bool] [default: false]")
+ − 382 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="plot only a chromosome [format: string]")
+ − 383 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start from a given region [format: int]")
+ − 384 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end from a given region [format: int]")
+ − 385 parser.add_option("-y", "--yMin", dest="yMin", action="store", default=None, type="int", help="minimum value on the y-axis to plot [format: int]")
+ − 386 parser.add_option("-Y", "--yMax", dest="yMax", action="store", default=None, type="int", help="maximum value on the y-axis to plot [format: int]")
+ − 387 parser.add_option("-x", "--csv", dest="csv", action="store", default=None, help="write a .csv file [format: output file in CSV format] [default: None]")
+ − 388 parser.add_option("-g", "--gff", dest="gff", action="store", default=None, help="also write GFF3 file [format: output file in GFF format] [default: None]")
+ − 389 parser.add_option("-H", "--height", dest="height", action="store", default=500, type="int", help="height of the graphics [format: int] [default: 300]")
+ − 390 parser.add_option("-W", "--width", dest="width", action="store", default=800, type="int", help="width of the graphics [format: int] [default: 1000]")
+ − 391 parser.add_option("-t", "--thickness", dest="lineThickness", action="store", default=1, type="int", help="thickness of the lines [format : int] [default : 1]")
+ − 392 parser.add_option("-d", "--policeLegend", dest="sizePoliceLegend", action="store", default=1.5, type="float", help="size of the police of the legend [format : float] [default : 1.5]")
+ − 393 parser.add_option("-D", "--dots", dest="dots", action="store_true", default=False, help="plot dots instead of lines [format : bool] [default : false]")
+ − 394 parser.add_option("-a", "--average", dest="average", action="store_true", default=False, help="plot average (instead of sum) [default: false] [format: boolean]")
+ − 395 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]")
+ − 396 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]")
+ − 397 parser.add_option("-z", "--normalize", dest="normalize", action="store_true", default=False, help="normalize data (when panels are different) [format: bool] [default: false]")
+ − 398 parser.add_option("-Z", "--normalizeFac", dest="normalizeFactors", action="store", default=None, help="normalize data with given factors (when panels are different) [format: string]")
+ − 399 parser.add_option("-m", "--merge", dest="mergePlots", action="store_true", default=False, help="merge all plots in one figure [format: bool] [default: false]")
+ − 400 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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+ − 401 (options, args) = parser.parse_args()
+ − 402
+ − 403 gt = GetDistribution(options.verbosity)
46
+ − 404 gt.setInputFiles(options.inputFileNames.split(","), options.format)
36
+ − 405 gt.setOutputFile(options.outputFileName)
+ − 406 gt.setReferenceFile(options.referenceFileName)
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+ − 407 gt.setNbBins(options.nbBins)
+ − 408 gt.setBinSize(options.binSize)
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+ − 409 gt.set2Strands(options.bothStrands)
+ − 410 gt.setRegion(options.chromosome, options.start, options.end)
+ − 411 gt.setNormalization(options.normalize)
+ − 412 gt.setAverage(options.average)
+ − 413 gt.setYLimits(options.yMin, options.yMax)
+ − 414 gt.writeCsv(options.csv)
+ − 415 gt.writeGff(options.gff)
+ − 416 gt.setImageSize(options.height, options.width)
+ − 417 gt.setNames(options.names.split(","))
46
+ − 418 gt.setThicknessCurve(options.lineThickness)
+ − 419 gt.setSizePoliceLegend(options.sizePoliceLegend)
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+ − 420 gt.setColors(None if options.colors == None else options.colors.split(","))
46
+ − 421 gt.setDots(options.dots)
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+ − 422 gt.setNormalization(options.normalize)
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+ − 423 gt.setNormalizationFactors(None if options.normalizeFactors == None else [float(factor) for factor in options.normalizeFactors.split(",")])
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+ − 424 gt.mergePlots(options.mergePlots)
+ − 425 gt.run()
+ − 426
