Mercurial > repos > yufei-luo > s_mart

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