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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.GffParser import GffParser
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37 from SMART.Java.Python.misc.RPlotter import RPlotter
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38 from SMART.Java.Python.misc.Progress import Progress
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39
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40
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41 if __name__ == "__main__":
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42
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43 # parse command line
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44 description = "Plot Repartition v1.0.1: Plot the repartition of different data on a whole genome. (This tool uses 1 input file only, the different values being stored in the tags. See documentation to know more about it.) [Category: Visualization]"
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45
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46 parser = OptionParser(description = description)
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47 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file name [compulsory] [format: file in GFF3 format]")
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48 parser.add_option("-n", "--names", dest="names", action="store", default=None, type="string", help="name for the tags (separated by commas and no space) [default: None] [format: string]")
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49 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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50 parser.add_option("-c", "--color", dest="colors", action="store", default=None, type="string", help="color of the lines (separated by commas and no space) [format: string]")
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51 parser.add_option("-f", "--format", dest="format", action="store", default="png", type="string", help="format of the output file [format: string] [default: png]")
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52 parser.add_option("-r", "--normalize", dest="normalize", action="store_true", default=False, help="normalize data (when panels are different) [format: bool] [default: false]")
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53 parser.add_option("-l", "--log", dest="log", action="store", default="", type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]")
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54 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [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 (options, args) = parser.parse_args()
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57
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58 strands = [1, -1]
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59 strandToString = {1: "+", -1: "-"}
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60 names = [None] if options.names == None else options.names.split(",")
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61 maxs = {}
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62 nbElements = [0 for name in names]
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63 lines = [{} for i in range(len(names))]
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64 if options.colors == None:
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65 colors = [None for i in range(len(names))]
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66 else:
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67 colors = options.colors.split(",")
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68
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69 parser = GffParser(options.inputFileName, options.verbosity)
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70 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (options.inputFileName), options.verbosity)
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71 for transcript in parser.getIterator():
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72 chromosome = transcript.getChromosome()
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73 direction = transcript.getDirection()
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74 start = transcript.getStart()
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75 for i, name in enumerate(names):
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76 if chromosome not in lines[i]:
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77 lines[i][chromosome] = dict([(strand, {}) for strand in strands])
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78 if chromosome not in maxs:
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79 maxs[chromosome] = transcript.getStart()
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80 else:
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81 maxs[chromosome] = max(maxs[chromosome], start)
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82 if start not in lines[i][chromosome][direction]:
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83 lines[i][chromosome][direction][start] = 0
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84 thisNbElements = float(transcript.getTagValue(name)) if name != None and name in transcript.getTagNames() else 1
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85 lines[i][chromosome][direction][start] += thisNbElements * direction
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86 nbElements[i] += thisNbElements
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87 progress.inc()
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88 progress.done()
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89
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90 if options.normalize:
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91 if options.verbosity >= 10:
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92 print "Normalizing..."
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93 for i, linesPerCondition in enumerate(lines):
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94 for linesPerChromosome in linesPerCondition.values():
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95 for line in linesPerChromosome.values():
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96 for key, value in line.iteritems():
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97 line[key] = value / float(nbElements[i]) * max(nbElements)
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98 if options.verbosity >= 10:
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99 print "... done."
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100
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101 progress = Progress(len(maxs.keys()), "Plotting", options.verbosity)
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102 for chromosome in maxs:
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103 plot = RPlotter("%s%s.%s" % (options.outputFileName, chromosome.capitalize(), options.format), options.verbosity)
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104 plot.setLog(options.log)
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105 plot.setImageSize(2000, 500)
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106 plot.setFormat(options.format)
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107 if maxs[chromosome] <= 1000:
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108 unit = "nt."
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109 ratio = 1.0
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110 elif maxs[chromosome] <= 1000000:
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111 unit = "kb"
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112 ratio = 1000.0
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113 else:
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114 unit = "Mb"
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115 ratio = 1000000.0
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116 plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
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117 plot.setYLabel("# reads")
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118 plot.setLegend(True)
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119 for i, name in enumerate(names):
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120 for strand in strands:
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121 correctedLine = dict([(key / ratio, value) for key, value in lines[i][chromosome][strand].iteritems()])
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122 if name != None:
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123 name = "%s (%s)" % (name.replace("_", " "), strandToString[strand])
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124 plot.addLine(correctedLine, None, colors[i])
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125 plot.plot()
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126 progress.inc()
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127 progress.done()
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128
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