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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Get the size distribution of a Fasta / BED file"""
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32
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33 import os
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34 from optparse import OptionParser
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35 from commons.core.parsing.FastaParser import *
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36 from SMART.Java.Python.misc.Progress import *
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37 from SMART.Java.Python.misc.RPlotter import *
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38 from commons.core.parsing.ParserChooser import ParserChooser
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39
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40
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41 def writeCVSfile(outHandler):
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42 for pos in range(len(letters)):
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43 posTrue = pos +1
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44 outHandler.write( "%s;" % (posTrue))
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45 for letter in lettersRate:
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46 if positionRate[letter].has_key(pos):
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47 outHandler.write("%s=%.2f%s;" %(letter, positionRate[letter][pos], "%"))
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48 else:
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49 outHandler.write("%s=0%s;" % (letter, "%"))
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50 outHandler.write("\n")
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51
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52 if __name__ == "__main__":
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53
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54 # parse command line
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55 description = "Get Letter Distribution v1.0.1: Compute the distribution of nucleotides of a set of genomic coordinates. [Category: Visualization]"
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56
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57 parser = OptionParser(description = description)
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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]")
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59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: sequence file format]")
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60 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
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61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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62 parser.add_option("-c", "--csv", dest="csv", action="store_true", default=False, help="write a .csv file [format: bool] [default: false]")
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63 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
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64 (options, args) = parser.parse_args()
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65
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66 chooser = ParserChooser()
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67 chooser.findFormat(options.format)
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68 parser = chooser.getParser(options.inputFileName)
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69 nbSequences = parser.getNbSequences()
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70 print "%i sequences read" % (nbSequences)
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71
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72 # treat items
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73 progress = Progress(nbSequences, "Analyzing sequences of " + options.inputFileName, options.verbosity)
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74 nbLettersTotal = 0
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75 nbLetters = {}
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76 lettersRate = {}
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77 nbPositions = {}
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78 positionCount = {}
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79 positionRate = {}
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80 nbPositionRate = {}
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81 for sequence in parser.getIterator():
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82 letters = sequence.getSequence()
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83 thisNbLettersTotal = sequence.getSize()
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84 nbLettersTotal += thisNbLettersTotal
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85 thisNbLetters = {}
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86
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87 for pos in range(len(letters)):
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88 letter = letters[pos]
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89 if letter not in thisNbLetters:
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90 thisNbLetters[letter] = 1
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91 else:
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92 thisNbLetters[letter] += 1
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93 if pos+1 not in nbPositions:
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94 nbPositions[pos+1] = 1
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95 else:
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96 nbPositions[pos+1] += 1
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97 if letter not in positionCount:
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98 positionCount[letter] = {}
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99 if pos+1 not in positionCount[letter]:
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100 positionCount[letter][pos+1] = 1
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101 else:
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102 positionCount[letter][pos+1] += 1
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103
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104 for letter in thisNbLetters:
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105 if letter not in nbLetters:
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106 nbLetters[letter] = thisNbLetters[letter]
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107 else:
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108 nbLetters[letter] += thisNbLetters[letter]
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109 if letter not in lettersRate:
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110 lettersRate[letter] = {}
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111 rate = int(float(thisNbLetters[letter]) / thisNbLettersTotal * 100)
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112 if rate not in lettersRate[letter]:
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113 lettersRate[letter][rate] = 1
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114 else:
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115 lettersRate[letter][rate] += 1
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116 progress.inc()
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117 progress.done()
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118
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119 for letter in positionCount:
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120 positionRate[letter] = {}
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121 for pos in positionCount[letter]:
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122 positionRate[letter][pos] = positionCount[letter][pos] / float(nbPositions[pos]) * 100
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123 for pos in nbPositions:
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124 nbPositionRate[pos] = nbPositions[pos] / float(nbPositions[1]) * 100
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125
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126 # plot content distributions
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127 plotter = RPlotter("%s.png" % (options.outputFileName), options.verbosity, True)
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128 plotter.setFill(0)
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129 plotter.setLegend(True)
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130 for letter in lettersRate:
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131 plotter.addLine(lettersRate[letter], letter)
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132 plotter.plot()
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133
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134 # plot distribution per position
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135 plotter = RPlotter("%sPerNt.png" % (options.outputFileName), options.verbosity, True)
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136 plotter.setFill(0)
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137 plotter.setLegend(True)
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138 plotter.setXLabel("Position on the read")
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139 plotter.setYLabel("Percentage")
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140 for letter in positionRate:
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141 plotter.addLine(positionRate[letter], letter)
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142 plotter.addLine(nbPositionRate, "#")
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143 plotter.plot()
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144
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145 if options.csv:
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146 outHandler = open("%s.csv" % (options.outputFileName), "w")
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147 writeCVSfile(outHandler)
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148 outHandler.close()
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149
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150 print "%d sequences" % (nbSequences)
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151 print "%d letters" % (nbLettersTotal)
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152 for letter in nbLetters:
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153 print "%s: %d (%.2f%%)" % (letter, nbLetters[letter], float(nbLetters[letter]) / nbLettersTotal * 100)
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