36
+ − 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 os, sys
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.FastaParser import FastaParser
+ − 34 from commons.core.parsing.FastqParser import FastqParser
+ − 35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 36 from commons.core.parsing.GffParser import GffParser
+ − 37 from SMART.Java.Python.misc.Progress import Progress
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39 from SMART.Java.Python.misc import Utils
+ − 40
+ − 41 from commons.core.LoggerFactory import LoggerFactory
+ − 42 from commons.core.utils.RepetOptionParser import RepetOptionParser
+ − 43
+ − 44 LOG_DEPTH = "smart"
+ − 45
+ − 46 class GetSizes(object):
+ − 47
+ − 48 def __init__(self, inFileName = None, inFormat=None, outFileName = None, query=None,xMax=None, xMin=None, verbosity = 0):
+ − 49 self.inFileName = inFileName
+ − 50 self.inFormat= inFormat
+ − 51 self.outFileName = outFileName
+ − 52 self.query = query
+ − 53 self.xMax = xMax
+ − 54 self.xMin = xMin
+ − 55 self.xLab = "Size"
+ − 56 self.yLab = "# reads"
+ − 57 self.barplot = False
+ − 58 self._verbosity = verbosity
+ − 59 self.parser = None
+ − 60 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+ − 61
+ − 62 def setAttributesFromCmdLine(self):
+ − 63 description = "Usage: getSizes.py [options]\n\nGet Sizes v1.0.2: Get the sizes of a set of genomic coordinates. [Category: Visualization]\n"
+ − 64 epilog = ""
+ − 65 parser = RepetOptionParser(description = description, epilog = epilog)
+ − 66 parser.add_option("-i", "--input", dest="inputFileName", action="store", default=None, type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]")
+ − 67 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]")
+ − 68 parser.add_option("-q", "--query", dest="query", action="store", default=None, type="string", help="type to mesure [default: size] [format: choice (size, intron size, exon size, 1st exon size)]")
+ − 69 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in PNG format]")
+ − 70 parser.add_option("-x", "--xMax", dest="xMax", action="store", default=None, type="int", help="maximum value on the x-axis to plot [format: int]")
+ − 71 parser.add_option("-X", "--xMin", dest="xMin", action="store", default=None, type="int", help="minimum value on the x-axis to plot [format: int]")
+ − 72 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 73 parser.add_option("-a", "--xLabel", dest="xLab", action="store", default="Size", type="string", help="x absis label name [format: string] [default: Size]")
+ − 74 parser.add_option("-b", "--yLabel", dest="yLab", action="store", default="# reads", type="string", help="y absis label name [format: string] [default: Reads]")
+ − 75 parser.add_option("-B", "--barplot", dest="barplot", action="store_true", default=False, help="use barplot representation [format: bool] [default: false]")
+ − 76 options = parser.parse_args()[0]
+ − 77 self._setAttributesFromOptions(options)
+ − 78
+ − 79 def _setAttributesFromOptions(self, options):
+ − 80 self.setInFileName(options.inputFileName)
+ − 81 self.setInFormat(options.format)
+ − 82 self.setQuery(options.query)
+ − 83 self.setOutFileName(options.outputFileName)
+ − 84 self.setXMax(options.xMax)
+ − 85 self.setXMin(options.xMin)
+ − 86 self.setxLab(options.xLab)
+ − 87 self.setyLab(options.yLab)
+ − 88 self.setBarplot(options.barplot)
+ − 89 self.setVerbosity(options.verbosity)
+ − 90
+ − 91 def setInFileName(self, inputFileName):
+ − 92 self.inFileName = inputFileName
+ − 93
+ − 94 def setInFormat(self, inFormat):
+ − 95 self.inFormat = inFormat
+ − 96
+ − 97 def setQuery(self, query):
+ − 98 self.query = query
+ − 99
+ − 100 def setOutFileName(self, outFileName):
+ − 101 self.outFileName = outFileName
+ − 102
+ − 103 def setXMax(self, xMax):
+ − 104 self.xMax = xMax
+ − 105
+ − 106 def setXMin(self, xMin):
+ − 107 self.xMin = xMin
+ − 108
+ − 109 def setxLab(self, xLab):
+ − 110 self.xLab = xLab
+ − 111
+ − 112 def setyLab(self, yLab):
+ − 113 self.yLab = yLab
+ − 114
+ − 115 def setBarplot(self, barplot):
+ − 116 self.barplot = barplot
+ − 117
+ − 118 def setVerbosity(self, verbosity):
+ − 119 self._verbosity = verbosity
+ − 120
+ − 121 def _checkOptions(self):
+ − 122 if self.inFileName == None:
+ − 123 self._logAndRaise("ERROR: Missing input file name")
+ − 124 if self.inFormat == "fasta":
+ − 125 self.parser = FastaParser(self.inFileName, self._verbosity)
+ − 126 elif self.inFormat == "fastq":
+ − 127 self.parser = FastqParser(self.inFileName, self._verbosity)
+ − 128 else:
+ − 129 self.parser = TranscriptContainer(self.inFileName, self.inFormat, self._verbosity)
+ − 130
+ − 131 def _logAndRaise(self, errorMsg):
+ − 132 self._log.error(errorMsg)
+ − 133 raise Exception(errorMsg)
+ − 134
+ − 135 def run(self):
+ − 136 LoggerFactory.setLevel(self._log, self._verbosity)
+ − 137 self._checkOptions()
+ − 138 self._log.info("START getsizes")
+ − 139 self._log.debug("Input file name: %s" % self.inFileName)
+ − 140
+ − 141 nbItems = self.parser.getNbItems()
+ − 142 self._log.info( "%i items found" % (nbItems))
+ − 143
+ − 144 # treat items
+ − 145 progress = Progress(nbItems, "Analyzing sequences of %s" % (self.inFileName), self._verbosity)
+ − 146 sizes = {}
+ − 147 minimum = 1000000000000
+ − 148 maximum = 0
+ − 149 sum = 0
+ − 150 number = 0
+ − 151 nbSubItems = 0
+ − 152 for item in self.parser.getIterator():
+ − 153 items = []
+ − 154 if self.query == "exon":
+ − 155 items = item.getExons()
+ − 156 elif self.query == "exon1":
+ − 157 if len(item.getExons()) > 1:
+ − 158 item.sortExons()
+ − 159 items = [item.getExons()[0]]
+ − 160 elif self.query == "intron":
+ − 161 items = item.getIntrons()
+ − 162 else:
+ − 163 items = [item, ]
+ − 164
+ − 165 for thisItem in items:
+ − 166 try:
+ − 167 nbElements = int(float(thisItem.getTagValue("nbElements")))
+ − 168 if nbElements == None:
+ − 169 nbElements = 1
+ − 170 except:
+ − 171 nbElements = 1
+ − 172 size = thisItem.getSize()
+ − 173 minimum = min(minimum, size)
+ − 174 maximum = max(maximum, size)
+ − 175
+ − 176 if size not in sizes:
+ − 177 sizes[size] = nbElements
+ − 178 else:
+ − 179 sizes[size] += nbElements
+ − 180 sum += size
+ − 181 nbSubItems += nbElements
+ − 182 number += 1
+ − 183 progress.inc()
+ − 184 progress.done()
+ − 185
+ − 186 if self.outFileName != None:
+ − 187 plotter = RPlotter(self.outFileName, self._verbosity)
+ − 188 plotter.setFill(0)
+ − 189 plotter.setMinimumX(self.xMin)
+ − 190 plotter.setMaximumX(self.xMax)
+ − 191 plotter.setXLabel(self.xLab)
+ − 192 plotter.setYLabel(self.yLab)
+ − 193 plotter.setBarplot(self.barplot)
+ − 194 plotter.addLine(sizes)
+ − 195 plotter.plot()
+ − 196
+ − 197 if nbSubItems == 0:
+ − 198 self._logAndRaise("No item found")
+ − 199
+ − 200 self.items = number
+ − 201 self.subItems = nbSubItems
+ − 202 self.nucleotides = sum
+ − 203 self.minAvgMedMax = Utils.getMinAvgMedMax(sizes)
+ − 204
+ − 205 print "%d items" % (number)
+ − 206 print "%d sub-items" % (nbSubItems)
+ − 207 print "%d nucleotides" % (sum)
+ − 208 print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(sizes)
+ − 209
+ − 210 self._log.info("END getsizes")
+ − 211
+ − 212
+ − 213 if __name__ == "__main__":
+ − 214 iGetSizes = GetSizes()
+ − 215 iGetSizes.setAttributesFromCmdLine()
+ − 216 iGetSizes.run()
+ − 217
+ − 218 #TODO: add two more options!!!!!!
