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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 """Get the size distribution of a Fasta / BED file"""
+ − 32
+ − 33 import os
+ − 34 from optparse import OptionParser
+ − 35 from commons.core.parsing.FastaParser import *
+ − 36 from SMART.Java.Python.misc.Progress import *
+ − 37 from SMART.Java.Python.misc.RPlotter import *
+ − 38 from commons.core.parsing.ParserChooser import ParserChooser
+ − 39
+ − 40
+ − 41 def writeCVSfile(outHandler):
+ − 42 for pos in range(len(letters)):
+ − 43 posTrue = pos +1
+ − 44 outHandler.write( "%s;" % (posTrue))
+ − 45 for letter in lettersRate:
+ − 46 if positionRate[letter].has_key(pos):
+ − 47 outHandler.write("%s=%.2f%s;" %(letter, positionRate[letter][pos], "%"))
+ − 48 else:
+ − 49 outHandler.write("%s=0%s;" % (letter, "%"))
+ − 50 outHandler.write("\n")
+ − 51
+ − 52 if __name__ == "__main__":
+ − 53
+ − 54 # parse command line
+ − 55 description = "Get Letter Distribution v1.0.1: Compute the distribution of nucleotides of a set of genomic coordinates. [Category: Visualization]"
+ − 56
+ − 57 parser = OptionParser(description = description)
+ − 58 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file to be analyzed [compulsory] [format: file in sequence format given by -f]")
+ − 59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: sequence file format]")
+ − 60 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
+ − 61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 62 parser.add_option("-c", "--csv", dest="csv", action="store_true", default=False, help="write a .csv file [format: bool] [default: false]")
+ − 63 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 64 (options, args) = parser.parse_args()
+ − 65
+ − 66 chooser = ParserChooser()
+ − 67 chooser.findFormat(options.format)
+ − 68 parser = chooser.getParser(options.inputFileName)
+ − 69 nbSequences = parser.getNbSequences()
+ − 70 print "%i sequences read" % (nbSequences)
+ − 71
+ − 72 # treat items
+ − 73 progress = Progress(nbSequences, "Analyzing sequences of " + options.inputFileName, options.verbosity)
+ − 74 nbLettersTotal = 0
+ − 75 nbLetters = {}
+ − 76 lettersRate = {}
+ − 77 nbPositions = {}
+ − 78 positionCount = {}
+ − 79 positionRate = {}
+ − 80 nbPositionRate = {}
+ − 81 for sequence in parser.getIterator():
+ − 82 letters = sequence.getSequence()
+ − 83 thisNbLettersTotal = sequence.getSize()
+ − 84 nbLettersTotal += thisNbLettersTotal
+ − 85 thisNbLetters = {}
+ − 86
+ − 87 for pos in range(len(letters)):
+ − 88 letter = letters[pos]
+ − 89 if letter not in thisNbLetters:
+ − 90 thisNbLetters[letter] = 1
+ − 91 else:
+ − 92 thisNbLetters[letter] += 1
+ − 93 if pos+1 not in nbPositions:
+ − 94 nbPositions[pos+1] = 1
+ − 95 else:
+ − 96 nbPositions[pos+1] += 1
+ − 97 if letter not in positionCount:
+ − 98 positionCount[letter] = {}
+ − 99 if pos+1 not in positionCount[letter]:
+ − 100 positionCount[letter][pos+1] = 1
+ − 101 else:
+ − 102 positionCount[letter][pos+1] += 1
+ − 103
+ − 104 for letter in thisNbLetters:
+ − 105 if letter not in nbLetters:
+ − 106 nbLetters[letter] = thisNbLetters[letter]
+ − 107 else:
+ − 108 nbLetters[letter] += thisNbLetters[letter]
+ − 109 if letter not in lettersRate:
+ − 110 lettersRate[letter] = {}
+ − 111 rate = int(float(thisNbLetters[letter]) / thisNbLettersTotal * 100)
+ − 112 if rate not in lettersRate[letter]:
+ − 113 lettersRate[letter][rate] = 1
+ − 114 else:
+ − 115 lettersRate[letter][rate] += 1
+ − 116 progress.inc()
+ − 117 progress.done()
+ − 118
+ − 119 for letter in positionCount:
+ − 120 positionRate[letter] = {}
+ − 121 for pos in positionCount[letter]:
+ − 122 positionRate[letter][pos] = positionCount[letter][pos] / float(nbPositions[pos]) * 100
+ − 123 for pos in nbPositions:
+ − 124 nbPositionRate[pos] = nbPositions[pos] / float(nbPositions[1]) * 100
+ − 125
+ − 126 # plot content distributions
+ − 127 plotter = RPlotter("%s.png" % (options.outputFileName), options.verbosity, True)
+ − 128 plotter.setFill(0)
+ − 129 plotter.setLegend(True)
+ − 130 for letter in lettersRate:
+ − 131 plotter.addLine(lettersRate[letter], letter)
+ − 132 plotter.plot()
+ − 133
+ − 134 # plot distribution per position
+ − 135 plotter = RPlotter("%sPerNt.png" % (options.outputFileName), options.verbosity, True)
+ − 136 plotter.setFill(0)
+ − 137 plotter.setLegend(True)
+ − 138 plotter.setXLabel("Position on the read")
+ − 139 plotter.setYLabel("Percentage")
+ − 140 for letter in positionRate:
+ − 141 plotter.addLine(positionRate[letter], letter)
+ − 142 plotter.addLine(nbPositionRate, "#")
+ − 143 plotter.plot()
+ − 144
+ − 145 if options.csv:
+ − 146 outHandler = open("%s.csv" % (options.outputFileName), "w")
+ − 147 writeCVSfile(outHandler)
+ − 148 outHandler.close()
+ − 149
+ − 150 print "%d sequences" % (nbSequences)
+ − 151 print "%d letters" % (nbLettersTotal)
+ − 152 for letter in nbLetters:
+ − 153 print "%s: %d (%.2f%%)" % (letter, nbLetters[letter], float(nbLetters[letter]) / nbLettersTotal * 100)