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+ − 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 """
+ − 32 Plot the data from the data files
+ − 33 """
+ − 34 import os
+ − 35 from optparse import OptionParser
+ − 36 from commons.core.parsing.FastaParser import FastaParser
+ − 37 from commons.core.parsing.FastqParser import FastqParser
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39 from SMART.Java.Python.misc.Progress import Progress
+ − 40 from SMART.Java.Python.misc import Utils
+ − 41
+ − 42
+ − 43 if __name__ == "__main__":
+ − 44
+ − 45 # parse command line
+ − 46 description = "Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. [Category: Visualization]"
+ − 47
+ − 48 parser = OptionParser(description = description)
+ − 49 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file sequence [compulsory] [format: file in sequence format given by -f]")
+ − 50 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the file [compulsory] [format: sequence file format]")
+ − 51 parser.add_option("-n", "--number", dest="number", action="store", default=None, type="int", help="keep the best n [format: int]")
+ − 52 parser.add_option("-p", "--percent", dest="percent", action="store", default=None, type="float", help="keep the best n\% [format: float]")
+ − 53 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output files in PNG format and txt format]")
+ − 54 parser.add_option("-x", "--xMax", dest="xMax", action="store", default=None, type="int", help="maximum value on the x-axis to plot [format: int]")
+ − 55 parser.add_option("-D", "--directory", dest="working_Dir", action="store", default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
+ − 56 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 57 (options, args) = parser.parse_args()
+ − 58
+ − 59 if options.working_Dir[-1] != '/':
+ − 60 options.outputFileName = options.working_Dir + '/' + options.outputFileName
+ − 61
+ − 62 if options.format == "fasta":
+ − 63 parser = FastaParser(options.inputFileName, options.verbosity)
+ − 64 elif options.format == "fastq":
+ − 65 parser = FastqParser(options.inputFileName, options.verbosity)
+ − 66 else:
+ − 67 raise Exception("Do not understand '%s' file format." % (options.format))
+ − 68
+ − 69 progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
+ − 70 sequences = {}
+ − 71 for sequence in parser.getIterator():
+ − 72 sequence = sequence.sequence
+ − 73 if sequence not in sequences:
+ − 74 sequences[sequence] = 1
+ − 75 else:
+ − 76 sequences[sequence] += 1
+ − 77 progress.inc()
+ − 78 progress.done()
+ − 79
+ − 80 values = sequences.values()
+ − 81 values.sort()
+ − 82 if options.percent != None:
+ − 83 threshold = values[int(float(options.percent) / 100 * len(values))]
+ − 84 elif options.number != None:
+ − 85 threshold = values[-options.number]
+ − 86 else:
+ − 87 threshold = 0
+ − 88
+ − 89 # sort by value
+ − 90 progress = Progress(parser.getNbSequences(), "Sorting values", options.verbosity)
+ − 91 sortedValues = dict([(value, []) for value in sequences.values()])
+ − 92 for sequence, value in sequences.iteritems():
+ − 93 sortedValues[value].append(sequence)
+ − 94 progress.inc()
+ − 95 progress.done()
+ − 96
+ − 97 outputFileName = "%s.txt" % (options.outputFileName)
+ − 98 handle = open(outputFileName, "w")
+ − 99 progress = Progress(parser.getNbSequences(), "Writing into %s" % (outputFileName), options.verbosity)
+ − 100 for value in reversed(sorted(sortedValues.keys())):
+ − 101 if value >= threshold:
+ − 102 for sequence in sortedValues[value]:
+ − 103 handle.write("%s\t%d\n" % (sequence, value))
+ − 104 progress.inc()
+ − 105 progress.done()
+ − 106 handle.close()
+ − 107
+ − 108 line = {}
+ − 109 progress = Progress(len(values), "Preparing plot", options.verbosity)
+ − 110 for value in values:
+ − 111 if value not in line:
+ − 112 line[value] = 1
+ − 113 else:
+ − 114 line[value] += 1
+ − 115 progress.inc()
+ − 116 progress.done()
+ − 117
+ − 118 plot = RPlotter("%s.png" % (options.outputFileName), options.verbosity)
+ − 119 plot.setFill(0)
+ − 120 plot.setMaximumX(options.xMax)
+ − 121 plot.setXLabel("# occurrences")
+ − 122 plot.setYLabel("# reads")
+ − 123 plot.addLine(line)
+ − 124 plot.plot()
+ − 125
+ − 126 if options.verbosity > 0:
+ − 127 print "%d/%.2f/%.1f/%d occurrences" % (Utils.getMinAvgMedMax(line))
+ − 128
+ − 129
