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comparison smart_toolShed/SMART/Java/Python/getLetterDistribution.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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 """Get the size distribution of a Fasta / BED file"""
32
33 import os
34 from optparse import OptionParser
35 from commons.core.parsing.FastaParser import *
36 from SMART.Java.Python.misc.Progress import *
37 from SMART.Java.Python.misc.RPlotter import *
38 from commons.core.parsing.ParserChooser import ParserChooser
39
40
41 def writeCVSfile(outHandler):
42 for pos in range(len(letters)):
43 posTrue = pos +1
44 outHandler.write( "%s;" % (posTrue))
45 for letter in lettersRate:
46 if positionRate[letter].has_key(pos):
47 outHandler.write("%s=%.2f%s;" %(letter, positionRate[letter][pos], "%"))
48 else:
49 outHandler.write("%s=0%s;" % (letter, "%"))
50 outHandler.write("\n")
51
52 if __name__ == "__main__":
53
54 # parse command line
55 description = "Get Letter Distribution v1.0.1: Compute the distribution of nucleotides of a set of genomic coordinates. [Category: Visualization]"
56
57 parser = OptionParser(description = description)
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]")
59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: sequence file format]")
60 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
62 parser.add_option("-c", "--csv", dest="csv", action="store_true", default=False, help="write a .csv file [format: bool] [default: false]")
63 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
64 (options, args) = parser.parse_args()
65
66 chooser = ParserChooser()
67 chooser.findFormat(options.format)
68 parser = chooser.getParser(options.inputFileName)
69 nbSequences = parser.getNbSequences()
70 print "%i sequences read" % (nbSequences)
71
72 # treat items
73 progress = Progress(nbSequences, "Analyzing sequences of " + options.inputFileName, options.verbosity)
74 nbLettersTotal = 0
75 nbLetters = {}
76 lettersRate = {}
77 nbPositions = {}
78 positionCount = {}
79 positionRate = {}
80 nbPositionRate = {}
81 for sequence in parser.getIterator():
82 letters = sequence.getSequence()
83 thisNbLettersTotal = sequence.getSize()
84 nbLettersTotal += thisNbLettersTotal
85 thisNbLetters = {}
86
87 for pos in range(len(letters)):
88 letter = letters[pos]
89 if letter not in thisNbLetters:
90 thisNbLetters[letter] = 1
91 else:
92 thisNbLetters[letter] += 1
93 if pos+1 not in nbPositions:
94 nbPositions[pos+1] = 1
95 else:
96 nbPositions[pos+1] += 1
97 if letter not in positionCount:
98 positionCount[letter] = {}
99 if pos+1 not in positionCount[letter]:
100 positionCount[letter][pos+1] = 1
101 else:
102 positionCount[letter][pos+1] += 1
103
104 for letter in thisNbLetters:
105 if letter not in nbLetters:
106 nbLetters[letter] = thisNbLetters[letter]
107 else:
108 nbLetters[letter] += thisNbLetters[letter]
109 if letter not in lettersRate:
110 lettersRate[letter] = {}
111 rate = int(float(thisNbLetters[letter]) / thisNbLettersTotal * 100)
112 if rate not in lettersRate[letter]:
113 lettersRate[letter][rate] = 1
114 else:
115 lettersRate[letter][rate] += 1
116 progress.inc()
117 progress.done()
118
119 for letter in positionCount:
120 positionRate[letter] = {}
121 for pos in positionCount[letter]:
122 positionRate[letter][pos] = positionCount[letter][pos] / float(nbPositions[pos]) * 100
123 for pos in nbPositions:
124 nbPositionRate[pos] = nbPositions[pos] / float(nbPositions[1]) * 100
125
126 # plot content distributions
127 plotter = RPlotter("%s.png" % (options.outputFileName), options.verbosity, True)
128 plotter.setFill(0)
129 plotter.setLegend(True)
130 for letter in lettersRate:
131 plotter.addLine(lettersRate[letter], letter)
132 plotter.plot()
133
134 # plot distribution per position
135 plotter = RPlotter("%sPerNt.png" % (options.outputFileName), options.verbosity, True)
136 plotter.setFill(0)
137 plotter.setLegend(True)
138 plotter.setXLabel("Position on the read")
139 plotter.setYLabel("Percentage")
140 for letter in positionRate:
141 plotter.addLine(positionRate[letter], letter)
142 plotter.addLine(nbPositionRate, "#")
143 plotter.plot()
144
145 if options.csv:
146 outHandler = open("%s.csv" % (options.outputFileName), "w")
147 writeCVSfile(outHandler)
148 outHandler.close()
149
150 print "%d sequences" % (nbSequences)
151 print "%d letters" % (nbLettersTotal)
152 for letter in nbLetters:
153 print "%s: %d (%.2f%%)" % (letter, nbLetters[letter], float(nbLetters[letter]) / nbLettersTotal * 100)