38
+ − 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 import random, os, glob, subprocess
+ − 32 from commons.core.parsing.ParserChooser import ParserChooser
+ − 33 from commons.core.parsing.GffParser import GffParser
+ − 34 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 35 from SMART.Java.Python.misc.Progress import Progress
+ − 36 from SMART.Java.Python.misc import Utils
+ − 37 from commons.core.LoggerFactory import LoggerFactory
+ − 38 from commons.core.utils.RepetOptionParser import RepetOptionParser
+ − 39
+ − 40 LOG_DEPTH = "smart"
+ − 41 DEFAULT_REGION = "_all_"
+ − 42 MULTIPLE_STR = {1: "", 1000: " (in kbp)", 1000000: " (in Gbp)"}
+ − 43
+ − 44 class GetReadDistribution(object):
+ − 45
+ − 46 def __init__(self, verbosity = 0):
+ − 47 self.xLab = ""
+ − 48 self.yLab = "# reads"
+ − 49 self.verbosity = verbosity
+ − 50 self.number = random.randint(0, 100000)
+ − 51 self.log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
+ − 52 self.parsers = {}
+ − 53 self.distribution = {}
+ − 54 self.factors = {}
+ − 55 self.regions = None
+ − 56 self.tmpDatName = None
+ − 57 self.tmpRName = None
+ − 58 self.quorum = 1
+ − 59 self.strands = False
+ − 60 self.width = 800
+ − 61 self.height = 300
+ − 62 self.arial = False
+ − 63
+ − 64 def setNames(self, names):
+ − 65 self.names = names
+ − 66
+ − 67 def setInputFiles(self, fileNames, format):
+ − 68 chooser = ParserChooser(self.verbosity)
+ − 69 chooser.findFormat(format)
+ − 70 for cpt, fileName in enumerate(fileNames):
+ − 71 self.parsers[self.names[cpt]] = chooser.getParser(fileName)
+ − 72
+ − 73 def setOutputFileName(self, fileName):
+ − 74 self.outputFileName = fileName
+ − 75
+ − 76 def setLabs(self, xLab, yLab):
+ − 77 self.xLab = xLab
+ − 78 self.yLab = yLab
+ − 79
+ − 80 def setBinSize(self, binSize):
+ − 81 self.binSize = binSize
+ − 82
+ − 83 def setColors(self, colors):
+ − 84 self.colors = colors
+ − 85
+ − 86 def setFactors(self, factors):
+ − 87 if factors == None:
+ − 88 self.factors = dict([name, 1.0] for name in self.names)
+ − 89 else:
+ − 90 self.factors = dict(zip(self.names, factors))
+ − 91
+ − 92 def setMultiple(self, boolean):
+ − 93 self.multiple = boolean
+ − 94
+ − 95 def setImageSize(self, width, height):
+ − 96 if width != None:
+ − 97 self.width = width
+ − 98 if height != None:
+ − 99 self.height = height
+ − 100
+ − 101 def setQuorum(self, quorum):
+ − 102 self.quorum = quorum
+ − 103
+ − 104 def setRegionsFile(self, fileName):
+ − 105 if fileName != None:
+ − 106 self._loadRegions(fileName)
+ − 107
+ − 108 def setBothStrands(self, strands):
+ − 109 self.strands = strands
+ − 110
+ − 111 def setArial(self, arial):
+ − 112 self.arial = arial
+ − 113
+ − 114 def _checkOptions(self):
+ − 115 if not self.parsers:
+ − 116 self.logAndRaise("ERROR: Missing input file names")
+ − 117
+ − 118 def _logAndRaise(self, errorMsg):
+ − 119 self.log.error(errorMsg)
+ − 120 raise Exception(errorMsg)
+ − 121
+ − 122 def _loadRegions(self, fileName):
+ − 123 self.regions = {}
+ − 124 parser = GffParser(fileName, self.verbosity)
+ − 125 for transcript in parser.getIterator():
+ − 126 chromosome = transcript.getChromosome()
+ − 127 start = transcript.getStart()
+ − 128 end = transcript.getEnd()
+ − 129 name = transcript.getName()
+ − 130 if chromosome not in self.regions:
+ − 131 self.regions[chromosome] = {}
+ − 132 if start not in self.regions[chromosome]:
+ − 133 self.regions[chromosome][start] = {}
+ − 134 if end not in self.regions[chromosome][start]:
+ − 135 self.regions[chromosome][start][end] = []
+ − 136 self.regions[chromosome][start][end].append(name)
+ − 137
+ − 138 def _getRegions(self, transcript):
+ − 139 if self.regions == None:
+ − 140 return [DEFAULT_REGION]
+ − 141 chromosome = transcript.getChromosome()
+ − 142 start = transcript.getStart()
+ − 143 end = transcript.getEnd()
+ − 144 if chromosome not in self.regions:
+ − 145 return []
+ − 146 names = []
+ − 147 for loadedStart in sorted(self.regions[chromosome].keys()):
+ − 148 if loadedStart > end:
+ − 149 return names
+ − 150 for loadedEnd in reversed(sorted(self.regions[chromosome][loadedStart].keys())):
+ − 151 if loadedEnd < start:
+ − 152 break
+ − 153 names.extend(self.regions[chromosome][loadedStart][loadedEnd])
+ − 154 return names
+ − 155
+ − 156 def _parse(self, name):
+ − 157 progress = UnlimitedProgress(10000, "Reading file '%s'" % (name), self.verbosity)
+ − 158 for transcript in self.parsers[name].getIterator():
+ − 159 if transcript.__class__.__name__ == "Mapping":
+ − 160 transcript = transcript.getTranscript()
+ − 161 regions = self._getRegions(transcript)
+ − 162 for region in regions:
+ − 163 if region not in self.distribution:
+ − 164 self.distribution[region] = {}
+ − 165 if name not in self.distribution[region]:
+ − 166 self.distribution[region][name] = {}
+ − 167 chromosome = transcript.getChromosome()
+ − 168 nbElements = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
+ − 169 nbElements *= self.factors.get(name, 1)
+ − 170 strand = transcript.getDirection() if self.strands else 1
+ − 171 if chromosome not in self.distribution[region][name]:
+ − 172 self.distribution[region][name][chromosome] = {}
+ − 173 if strand not in self.distribution[region][name][chromosome]:
+ − 174 self.distribution[region][name][chromosome][strand] = {}
+ − 175 previousBin = None
+ − 176 for exon in transcript.getExons():
+ − 177 for pos in range(exon.getStart(), exon.getEnd()+1):
+ − 178 bin = pos / self.binSize
+ − 179 if bin != previousBin:
+ − 180 self.distribution[region][name][chromosome][strand][bin] = self.distribution[region][name][chromosome][strand].get(bin, 0) + nbElements
+ − 181 previousBin = bin
+ − 182 progress.inc()
+ − 183 progress.done()
+ − 184
+ − 185 def _checkQuorum(self, region):
+ − 186 if self.quorum == None:
+ − 187 return True
+ − 188 return max([max([max([max(self.distribution[region][name][chromosome][strand].values()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]])
+ − 189
+ − 190 def _writeData(self, region):
+ − 191 self.tmpDatName = "tmpFile%d.dat" % (self.number)
+ − 192 handle = open(self.tmpDatName, "w")
+ − 193 handle.write("Chr\tPos\tStrand\tCount\tSample\n")
+ − 194 for name in self.distribution[region]:
+ − 195 for chromosome in sorted(self.distribution[region][name].keys()):
+ − 196 for strand in sorted(self.distribution[region][name][chromosome].keys()):
+ − 197 for pos in sorted(self.distribution[region][name][chromosome][strand].keys()):
+ − 198 handle.write("%s\t%d\t%d\t%d\t\"%s\"\n" % (chromosome, pos * self.binSize, strand, self.distribution[region][name][chromosome][strand].get(pos, 0) * strand, name))
+ − 199 handle.close()
+ − 200
+ − 201 def _findMultiple(self, region):
+ − 202 if not self.multiple:
+ − 203 return 1
+ − 204 maxPosition = max([max([max([max(self.distribution[region][name][chromosome][strand].keys()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]]) * self.binSize
+ − 205 if maxPosition > 2000000:
+ − 206 return 1000000
+ − 207 elif maxPosition > 2000:
+ − 208 return 1000
+ − 209 return 1
+ − 210
+ − 211 def _writeScript(self, region):
+ − 212 self.tmpRName = "tmpFile%d.R" % (self.number)
+ − 213 fileName = self.outputFileName if region == DEFAULT_REGION else "%s_%s.png" % (os.path.splitext(self.outputFileName)[0], region)
+ − 214 colors = "scale_fill_brewer(palette=\"Set1\") + scale_color_brewer(palette=\"Set1\")" if self.colors == None else "scale_fill_manual(values = c(%s)) + scale_color_manual(values = c(%s))" % (", ".join(["\"%s\"" % (color) for color in self.colors]), ", ".join(["\"%s\"" % (color) for color in self.colors]))
+ − 215 title = "" if region == DEFAULT_REGION else " + labs(title = \"Distribution of %s\") " % (region)
+ − 216 facet = "Sample ~ Chr" if region == DEFAULT_REGION else "Sample ~ ."
+ − 217 handle = open(self.tmpRName, "w")
+ − 218 multiple = self._findMultiple(region)
+ − 219 arial = ", text = element_text(family=\"Arial\", size=20)" if self.arial else ""
+ − 220 if self.arial:
+ − 221 handle.write("library(extrafont)\nloadfonts()\n")
+ − 222 handle.write("library(ggplot2)\n")
+ − 223 handle.write("data <- read.table(\"%s\", header = T)\n" % (self.tmpDatName))
+ − 224 handle.write("data$Sample <- factor(data$Sample, levels=c(%s))\n" % (", ".join(["\"%s\"" % (name) for name in self.names])))
+ − 225 handle.write("png(\"%s\", width = %d, height = %d)\n" % (fileName, self.width, self.height))
+ − 226 handle.write("ggplot(data, aes(x = Pos/%d, y = Count, fill = Sample, color = Sample)) %s + geom_bar(stat = \"identity\") + facet_grid(%s, space=\"free\") + xlab(\"%s%s\") + ylab(\"%s\") + %s + theme(legend.position = \"none\", panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()%s)\n" % (multiple, title, facet, self.xLab, MULTIPLE_STR[multiple], self.yLab, colors, arial))
+ − 227 handle.write("dev.off()\n")
+ − 228
+ − 229 def _runR(self):
+ − 230 rCommand = os.environ["SMARTRPATH"] if "SMARTRPATH" in os.environ else "R"
+ − 231 command = "\"%s\" CMD BATCH %s" % (rCommand, self.tmpRName)
+ − 232 status = subprocess.call(command, shell=True)
+ − 233 if status != 0:
+ − 234 raise Exception("Problem with the execution of script file %s, status is: %s" % (self.tmpRName, status))
+ − 235
+ − 236 def _plot(self):
+ − 237 progress = Progress(len(self.distribution), "Plotting data", self.verbosity)
+ − 238 for region in self.distribution:
+ − 239 if not self._checkQuorum(region):
+ − 240 self.log.info("Not displaying '%s' for it contains insufficient data." % (region))
+ − 241 else:
+ − 242 self._writeData(region)
+ − 243 self._writeScript(region)
+ − 244 self._runR()
+ − 245 progress.inc()
+ − 246 progress.done()
+ − 247
+ − 248 def _cleanFiles(self):
+ − 249 for fileName in (self.tmpDatName, self.tmpRName):
+ − 250 if fileName != None and os.path.exists(fileName):
+ − 251 os.remove(fileName)
+ − 252 for otherFileName in glob.glob("%s*" % (fileName)):
+ − 253 os.remove(otherFileName)
+ − 254
+ − 255 def run(self):
+ − 256 LoggerFactory.setLevel(self.log, self.verbosity)
+ − 257 self._checkOptions()
+ − 258 self.log.info("START Get Read Distribution")
+ − 259 for name in self.names:
+ − 260 self._parse(name)
+ − 261 self._plot()
+ − 262 self._cleanFiles()
+ − 263 self.log.info("END Get Read Distribution")
+ − 264
+ − 265
+ − 266 if __name__ == "__main__":
+ − 267 description = "Usage: GetReadDistribution.py [options]\n\nGet Read Distribution v1.0.1: Get the distribution of a set of reads. [Category: Personal]\n"
+ − 268 epilog = ""
+ − 269 parser = RepetOptionParser(description = description, epilog = epilog)
+ − 270 parser.add_option("-i", "--input", dest="inputFileNames", action="store", default=None, type="string", help="input files, separated by commas [compulsory] [format: string]")
+ − 271 parser.add_option("-f", "--format", dest="format", action="store", default=None, type="string", help="format of the input [compulsory] [format: transcript or sequence file format]")
+ − 272 parser.add_option("-n", "--names", dest="names", action="store", default=None, type="string", help="name of the input data, separated by commas [compulsory] [format: string]")
+ − 273 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in PNG format]")
+ − 274 parser.add_option("-s", "--binSize", dest="binSize", action="store", default=10000, type="int", help="bin size [format: int] [default: 10000]")
+ − 275 parser.add_option("-l", "--xLabel", dest="xLab", action="store", default="", type="string", help="x-axis label name [format: string]")
+ − 276 parser.add_option("-L", "--yLabel", dest="yLab", action="store", default="# reads", type="string", help="y-axis label name [format: string] [default: Reads]")
+ − 277 parser.add_option("-c", "--colors", dest="colors", action="store", default=None, type="string", help="colors of the bars, separated by commas [format: string]")
+ − 278 parser.add_option("-a", "--factors", dest="factors", action="store", default=None, type="string", help="normalization factors, separated by commas [format: string]")
+ − 279 parser.add_option("-r", "--regions", dest="regionsFileName", action="store", default=None, type="string", help="regions to plot [format: transcript file in GFF format]")
+ − 280 parser.add_option("-2", "--strands", dest="strands", action="store_true", default=False, help="plot negative strands on the negative x-axis [format: boolean] [default: False]")
+ − 281 parser.add_option("-m", "--multiple", dest="multiple", action="store_true", default=False, help="use human readable genomic positions (k, G) [format: boolean] [default: False]")
+ − 282 parser.add_option("-q", "--quorum", dest="quorum", action="store", default=1, type="int", help="minimum number of intervals to plot a region [format: int] [default: 1]")
+ − 283 parser.add_option("-z", "--width", dest="width", action="store", default=800, type="int", help="width of the image [format: int] [default: 800]")
+ − 284 parser.add_option("-Z", "--height", dest="height", action="store", default=300, type="int", help="height of the image [format: int] [default: 300]")
+ − 285 parser.add_option("-A", "--arial", dest="arial", action="store_true", default=False, help="use Arial font [format: boolean] [default: false]")
+ − 286 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 287 options = parser.parse_args()[0]
+ − 288 iGetReadDistribution = GetReadDistribution(options.verbosity)
+ − 289 iGetReadDistribution.setNames(options.names.split(","))
+ − 290 iGetReadDistribution.setInputFiles(options.inputFileNames.split(","), options.format)
+ − 291 iGetReadDistribution.setOutputFileName(options.outputFileName)
+ − 292 iGetReadDistribution.setLabs(options.xLab, options.yLab)
+ − 293 iGetReadDistribution.setBinSize(options.binSize)
+ − 294 iGetReadDistribution.setColors(None if options.colors == None else options.colors.split(","))
+ − 295 iGetReadDistribution.setFactors(None if options.factors == None else map(float, options.factors.split(",")))
+ − 296 iGetReadDistribution.setRegionsFile(options.regionsFileName)
+ − 297 iGetReadDistribution.setMultiple(options.multiple)
+ − 298 iGetReadDistribution.setQuorum(options.quorum)
+ − 299 iGetReadDistribution.setImageSize(options.width, options.height)
+ − 300 iGetReadDistribution.setBothStrands(options.strands)
+ − 301 iGetReadDistribution.setArial(options.arial)
+ − 302 iGetReadDistribution.run()
+ − 303
