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comparison SMART/Java/Python/plotRepartition.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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.GffParser import GffParser
37 from SMART.Java.Python.misc.RPlotter import RPlotter
38 from SMART.Java.Python.misc.Progress import Progress
39
40
41 if __name__ == "__main__":
42
43 # parse command line
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]"
45
46 parser = OptionParser(description = description)
47 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file name [compulsory] [format: file in GFF3 format]")
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]")
49 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
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]")
51 parser.add_option("-f", "--format", dest="format", action="store", default="png", type="string", help="format of the output file [format: string] [default: png]")
52 parser.add_option("-r", "--normalize", dest="normalize", action="store_true", default=False, help="normalize data (when panels are different) [format: bool] [default: false]")
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]")
54 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [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 (options, args) = parser.parse_args()
57
58 strands = [1, -1]
59 strandToString = {1: "+", -1: "-"}
60 names = [None] if options.names == None else options.names.split(",")
61 maxs = {}
62 nbElements = [0 for name in names]
63 lines = [{} for i in range(len(names))]
64 if options.colors == None:
65 colors = [None for i in range(len(names))]
66 else:
67 colors = options.colors.split(",")
68
69 parser = GffParser(options.inputFileName, options.verbosity)
70 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (options.inputFileName), options.verbosity)
71 for transcript in parser.getIterator():
72 chromosome = transcript.getChromosome()
73 direction = transcript.getDirection()
74 start = transcript.getStart()
75 for i, name in enumerate(names):
76 if chromosome not in lines[i]:
77 lines[i][chromosome] = dict([(strand, {}) for strand in strands])
78 if chromosome not in maxs:
79 maxs[chromosome] = transcript.getStart()
80 else:
81 maxs[chromosome] = max(maxs[chromosome], start)
82 if start not in lines[i][chromosome][direction]:
83 lines[i][chromosome][direction][start] = 0
84 thisNbElements = float(transcript.getTagValue(name)) if name != None and name in transcript.getTagNames() else 1
85 lines[i][chromosome][direction][start] += thisNbElements * direction
86 nbElements[i] += thisNbElements
87 progress.inc()
88 progress.done()
89
90 if options.normalize:
91 if options.verbosity >= 10:
92 print "Normalizing..."
93 for i, linesPerCondition in enumerate(lines):
94 for linesPerChromosome in linesPerCondition.values():
95 for line in linesPerChromosome.values():
96 for key, value in line.iteritems():
97 line[key] = value / float(nbElements[i]) * max(nbElements)
98 if options.verbosity >= 10:
99 print "... done."
100
101 progress = Progress(len(maxs.keys()), "Plotting", options.verbosity)
102 for chromosome in maxs:
103 plot = RPlotter("%s%s.%s" % (options.outputFileName, chromosome.capitalize(), options.format), options.verbosity)
104 plot.setLog(options.log)
105 plot.setImageSize(2000, 500)
106 plot.setFormat(options.format)
107 if maxs[chromosome] <= 1000:
108 unit = "nt."
109 ratio = 1.0
110 elif maxs[chromosome] <= 1000000:
111 unit = "kb"
112 ratio = 1000.0
113 else:
114 unit = "Mb"
115 ratio = 1000000.0
116 plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
117 plot.setYLabel("# reads")
118 plot.setLegend(True)
119 for i, name in enumerate(names):
120 for strand in strands:
121 correctedLine = dict([(key / ratio, value) for key, value in lines[i][chromosome][strand].iteritems()])
122 if name != None:
123 name = "%s (%s)" % (name.replace("_", " "), strandToString[strand])
124 plot.addLine(correctedLine, None, colors[i])
125 plot.plot()
126 progress.inc()
127 progress.done()
128