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