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 repartition of some elements in a chromosomes"""
+ − 32
+ − 33 import os
+ − 34 from optparse import OptionParser
+ − 35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 36 from SMART.Java.Python.structure.Transcript import Transcript
+ − 37 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39 from SMART.Java.Python.misc.Progress import Progress
+ − 40 from math import *
+ − 41
+ − 42 def divideKeyDict(dictionary, ratio):
+ − 43 return dict([(key / ratio, dictionary[key]) for key in dictionary])
+ − 44
+ − 45
+ − 46 def setTranscript(chromosome, direction, start, end, name, value):
+ − 47 transcript = Transcript()
+ − 48 transcript.setChromosome(chromosome)
+ − 49 transcript.setDirection(direction)
+ − 50 transcript.setStart(start)
+ − 51 transcript.setEnd(end)
+ − 52 transcript.setName(name)
+ − 53 transcript.setTagValue("nbElements", value)
+ − 54 return transcript
+ − 55
+ − 56
+ − 57
+ − 58 if __name__ == "__main__":
+ − 59
+ − 60 magnifyingFactor = 1000
+ − 61
+ − 62 # parse command line
+ − 63 description = "Get Distribution v1.0.1: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
+ − 64
+ − 65 parser = OptionParser(description = description)
+ − 66 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 67 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
+ − 68 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 69 parser.add_option("-r", "--reference", dest="referenceFileName", action="store", default=None, type="string", help="file containing the genome [compulsory] [format: file in FASTA format]")
+ − 70 parser.add_option("-n", "--nbBins", dest="nbBins", action="store", default=1000, type="int", help="number of bins [default: 1000] [format: int]")
+ − 71 parser.add_option("-2", "--bothStrands", dest="bothStrands", action="store_true", default=False, help="plot one curve per strand [format: bool] [default: false]")
+ − 72 parser.add_option("-w", "--raw", dest="raw", action="store_true", default=False, help="plot raw number of occurrences instead of density [format: bool] [default: false]")
+ − 73 parser.add_option("-x", "--csv", dest="csv", action="store_true", default=False, help="write a .csv file [format: bool]")
+ − 74 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="plot only a chromosome [format: string]")
+ − 75 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start from a given region [format: int]")
+ − 76 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end from a given region [format: int]")
+ − 77 parser.add_option("-y", "--yMin", dest="yMin", action="store", default=None, type="int", help="minimum value on the y-axis to plot [format: int]")
+ − 78 parser.add_option("-Y", "--yMax", dest="yMax", action="store", default=None, type="int", help="maximum value on the y-axis to plot [format: int]")
+ − 79 parser.add_option("-g", "--gff", dest="gff", action="store_true", default=False, help="also write GFF3 file [format: bool] [default: false]")
+ − 80 parser.add_option("-H", "--height", dest="height", action="store", default=None, type="int", help="height of the graphics [format: int] [default: 300]")
+ − 81 parser.add_option("-W", "--width", dest="width", action="store", default=None, type="int", help="width of the graphics [format: int] [default: 1000]")
+ − 82 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
+ − 83 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool]")
+ − 84 parser.add_option("-D", "--directory", dest="working_Dir", action="store", default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
+ − 85 (options, args) = parser.parse_args()
+ − 86
+ − 87 sizes = {}
+ − 88 if options.referenceFileName != None:
+ − 89 # get the sizes of the chromosomes
+ − 90 referenceHandle = open(options.referenceFileName)
+ − 91 name = None
+ − 92 size = 0
+ − 93 maxSize = 0
+ − 94 for line in referenceHandle:
+ − 95 line = line.strip()
+ − 96 if line == "": continue
+ − 97 if line[0] == ">":
+ − 98 if name != None:
+ − 99 if options.verbosity > 10:
+ − 100 print name
+ − 101 sizes[name] = size
+ − 102 maxSize = max(maxSize, size)
+ − 103 size = 0
+ − 104 name = line[1:]
+ − 105 else:
+ − 106 size += len(line)
+ − 107 sizes[name] = size
+ − 108 maxSize = max(maxSize, size)
+ − 109 if options.verbosity > 1:
+ − 110 print "done"
+ − 111 start = 0
+ − 112 end = maxSize
+ − 113 else:
+ − 114 if options.chromosome == None or options.start == None or options.end == None:
+ − 115 raise Exception("Missing chromosome or start and end positions, or reference file")
+ − 116 maxSize = options.end
+ − 117 sizes[options.chromosome] = options.end
+ − 118 start = options.start
+ − 119 end = options.end
+ − 120
+ − 121
+ − 122 tmp1 = int(maxSize / float(options.nbBins))
+ − 123 tmp2 = 10 ** (len("%d" % (tmp1))-2)
+ − 124 sliceSize = int((tmp1 / tmp2) * tmp2)
+ − 125
+ − 126 bins = dict()
+ − 127 binsPlus = dict()
+ − 128 binsMinus = dict()
+ − 129 for chromosome in sizes:
+ − 130 bins[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+ − 131 binsPlus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+ − 132 binsMinus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+ − 133
+ − 134 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+ − 135 progress = Progress(parser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+ − 136 maxSlice = 0
+ − 137 # count the number of reads
+ − 138 for transcript in parser.getIterator():
+ − 139 if options.chromosome == None or (transcript.getChromosome() == options.chromosome and transcript.getStart() >= start and transcript.getStart() <= end):
+ − 140 if transcript.getDirection() == 1:
+ − 141 binsPlus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+ − 142 else:
+ − 143 binsMinus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+ − 144 bins[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+ − 145 maxSlice = max(maxSlice, transcript.getStart() / sliceSize)
+ − 146 progress.inc()
+ − 147 progress.done()
+ − 148
+ − 149 # compute densities
+ − 150 densityPlus = dict()
+ − 151 for chromosome in bins:
+ − 152 densityPlus[chromosome] = dict([(bin, 0) for bin in binsPlus[chromosome]])
+ − 153 for bin in binsPlus[chromosome]:
+ − 154 densityPlus[chromosome][bin] = float(binsPlus[chromosome][bin]) / sliceSize * magnifyingFactor
+ − 155 # correct densities for first and last bins
+ − 156 if start % sliceSize != 0:
+ − 157 densityPlus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
+ − 158 if sizes[chromosome] % sliceSize != 0:
+ − 159 densityPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
+ − 160 densityMinus = dict()
+ − 161 for chromosome in binsMinus:
+ − 162 densityMinus[chromosome] = dict([(bin, 0) for bin in binsMinus[chromosome]])
+ − 163 for bin in binsMinus[chromosome]:
+ − 164 densityMinus[chromosome][bin] = float(binsMinus[chromosome][bin]) / sliceSize * magnifyingFactor
+ − 165 # correct densities for first and last bins
+ − 166 if start % sliceSize != 0:
+ − 167 densityMinus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
+ − 168 if sizes[chromosome] % sliceSize != 0:
+ − 169 densityMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
+ − 170 density = dict()
+ − 171 for chromosome in bins:
+ − 172 density[chromosome] = dict([(bin, 0) for bin in bins[chromosome]])
+ − 173 for bin in bins[chromosome]:
+ − 174 density[chromosome][bin] = densityPlus[chromosome][bin] + densityMinus[chromosome][bin]
+ − 175
+ − 176 for chromosome in densityMinus:
+ − 177 for bin in densityMinus[chromosome]:
+ − 178 densityMinus[chromosome][bin] *= -1
+ − 179 for bin in binsMinus[chromosome]:
+ − 180 binsMinus[chromosome][bin] *= -1
+ − 181
+ − 182 for chromosome in density:
+ − 183 maxX = max(bins[chromosome].keys())
+ − 184 if maxX <= 1000:
+ − 185 unit = "nt."
+ − 186 ratio = 1.0
+ − 187 elif maxX <= 1000000:
+ − 188 unit = "kb"
+ − 189 ratio = 1000.0
+ − 190 else:
+ − 191 unit = "Mb"
+ − 192 ratio = 1000000.0
+ − 193 outputFileName = "%s_%s" % (options.outputFileName, chromosome)
+ − 194 if options.start != None and options.end != None:
+ − 195 outputFileName += ":%d-%d" % (options.start, options.end)
+ − 196 outputFileName += ".png"
+ − 197 plotter = RPlotter(outputFileName, options.verbosity)
+ − 198 plotter.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
+ − 199 plotter.setYLabel("# reads")
+ − 200 if options.bothStrands:
+ − 201 plotter.setImageSize(1000, 300)
+ − 202 else:
+ − 203 plotter.setImageSize(1000, 200)
+ − 204 if options.height != None:
+ − 205 plotter.setHeight(options.height)
+ − 206 if options.width != None:
+ − 207 plotter.setWidth(options.width)
+ − 208 if options.yMax != None:
+ − 209 plotter.setMinimumY(options.yMin)
+ − 210 if options.yMax != None:
+ − 211 plotter.setMaximumY(options.yMax)
+ − 212 if options.bothStrands :
+ − 213 if options.raw:
+ − 214 plotter.addLine(divideKeyDict(binsPlus[chromosome], ratio))
+ − 215 else:
+ − 216 plotter.addLine(divideKeyDict(densityPlus[chromosome], ratio))
+ − 217 if options.raw:
+ − 218 plotter.addLine(divideKeyDict(binsMinus[chromosome], ratio))
+ − 219 else:
+ − 220 plotter.addLine(divideKeyDict(densityMinus[chromosome], ratio))
+ − 221 else:
+ − 222 if options.raw:
+ − 223 plotter.addLine(divideKeyDict(bins[chromosome], ratio))
+ − 224 else:
+ − 225 plotter.addLine(divideKeyDict(density[chromosome], ratio))
+ − 226 plotter.plot()
+ − 227
+ − 228 if options.csv:
+ − 229 outputFileName = "%s" % (options.outputFileName)
+ − 230 if options.chromosome != None:
+ − 231 outputFileName += "_%s" % (options.chromosome)
+ − 232 if options.start != None and options.end != None:
+ − 233 outputFileName += ":%d-%d" % (options.start, options.end)
+ − 234 outputFileName += ".csv"
+ − 235 csvHandle = open(outputFileName, "w")
+ − 236 for slice in range(start / sliceSize, maxSlice + 1):
+ − 237 csvHandle.write(";%d-%d" % (slice * sliceSize + 1, (slice+1) * sliceSize))
+ − 238 csvHandle.write("\n")
+ − 239 if options.bothStrands:
+ − 240 for chromosome in densityPlus:
+ − 241 if len(densityPlus[chromosome]) > 0:
+ − 242 csvHandle.write("%s [+]" % (chromosome))
+ − 243 for slice in sorted(densityPlus[chromosome].keys()):
+ − 244 csvHandle.write(";%.2f" % (densityPlus[chromosome][slice]))
+ − 245 csvHandle.write("\n")
+ − 246 if len(densityMinus[chromosome]) > 0:
+ − 247 csvHandle.write("%s [-]" % (chromosome))
+ − 248 for slice in sorted(densityPlus[chromosome].keys()):
+ − 249 csvHandle.write(";%.2f" % (-densityMinus[chromosome][slice]))
+ − 250 csvHandle.write("\n")
+ − 251 else:
+ − 252 for chromosome in density:
+ − 253 if len(density[chromosome]) > 0:
+ − 254 csvHandle.write(chromosome)
+ − 255 for slice in sorted(density[chromosome].keys()):
+ − 256 csvHandle.write(";%.2f" % (density[chromosome][slice]))
+ − 257 csvHandle.write("\n")
+ − 258 csvHandle.close()
+ − 259
+ − 260 if options.gff:
+ − 261 chromosome = "" if options.chromosome == None else options.chromosome.capitalize()
+ − 262 start = "" if options.start == None else "%d" % (options.start)
+ − 263 end = "" if options.end == None else "%d" % (options.end)
+ − 264 link1 = "" if options.start == None and options.end == None else ":"
+ − 265 link2 = "" if options.start == None and options.end == None else "-"
+ − 266 writer = Gff3Writer("%s%s%s%s%s.gff3" % (options.outputFileName, link1, start, link2, end), options.verbosity)
+ − 267 cpt = 1
+ − 268 if options.raw:
+ − 269 valuesPlus = binsPlus
+ − 270 valuesMinus = binsMinus
+ − 271 values = bins
+ − 272 else:
+ − 273 valuesPlus = densityPlus
+ − 274 valuesMinus = densityMinus
+ − 275 values = density
+ − 276 if options.bothStrands:
+ − 277 for chromosome in values:
+ − 278 for slice in valuesPlus[chromosome]:
+ − 279 writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), valuesPlus[chromosome][slice]))
+ − 280 cpt += 1
+ − 281 for slice in valuesMinus[chromosome]:
+ − 282 writer.addTranscript(setTranscript(chromosome, -1, slice, slice + sliceSize, "region%d" % (cpt), - valuesMinus[chromosome][slice]))
+ − 283 cpt += 1
+ − 284 else:
+ − 285 for chromosome in values:
+ − 286 for slice in values[chromosome]:
+ − 287 writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), values[chromosome][slice]))
+ − 288 cpt += 1
+ − 289 writer.write()
+ − 290
+ − 291
