annotate SMART/Java/Python/getWigProfile.py @ 28:2a3fdec156e0

Deleted selected files
author m-zytnicki
date Mon, 29 Apr 2013 03:31:52 -0400
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 #! /usr/bin/env python
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 # Copyright INRA-URGI 2009-2010
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 import math
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 from optparse import OptionParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 from commons.core.parsing.WigParser import WigParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 from SMART.Java.Python.misc.Progress import Progress
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 from SMART.Java.Python.misc.RPlotter import RPlotter
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 class GetWigProfile(object):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 def __init__(self, verbosity):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 self.verbosity = verbosity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 self.values = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 self.defaultValue = 0.0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 def _iToJ(self, i, size):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 return min(self.nbPoints+1, int(math.floor(float(i - self.distance) / (size) * (self.nbPoints))))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 def readTranscripts(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 self.strandNames = (1, -1) if self.strands else (1, )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 self.values = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 transcriptParser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 wigParser = WigParser(self.wig)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 nbValues = dict([(strand, dict([(i, 0.0) for i in range(self.nbPoints + 2 * self.distance)])) for strand in self.strandNames])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 wigParser.setStrands(self.strands)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 wigParser.setDefaultValue(self.defaultValue)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (self.inputFileName), self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 for transcript in transcriptParser.getIterator():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 transcriptSize = transcript.getSize()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 expectedSize = transcriptSize + 2 * self.distance
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 transcript.extendStart(self.distance)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 transcript.extendEnd(self.distance)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 theseValues = transcript.extractWigData(wigParser)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 if len(self.strandNames) == 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 theseValues = {1: theseValues}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 for strand in self.strandNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 if len(theseValues[strand]) < expectedSize:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73 theseValues[strand] = [self.defaultValue] * (expectedSize - len(theseValues[strand])) + theseValues[strand]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 if len(theseValues[strand]) != expectedSize:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 raise Exception("Got something wrong with the size of the WIG data concerning %s [%s]: %d found instead of %d" % (transcript, ",".join(["%d-%d" % (exon.getStart(), exon.getEnd()) for exon in transcript.getExons()]), len(theseValues[strand]), expectedSize))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 fivePValues = theseValues[strand][: self.distance]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 nbValues = [0.0] * (self.nbPoints)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 transcriptValues = [0.0] * (self.nbPoints)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 for i in range(self.distance, len(theseValues[strand]) - self.distance):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 startJ = self._iToJ(i, transcriptSize)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 endJ = max(startJ+1, self._iToJ(i+1, transcriptSize))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 for j in range(startJ, endJ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 transcriptValues[j] += theseValues[strand][i]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 nbValues[j] += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 threePValues = theseValues[strand][-self.distance: ]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86 values = fivePValues + [self.defaultValue if nbValue == 0 else transcriptValue / nbValue for transcriptValue, nbValue in zip(transcriptValues, nbValues)] + threePValues
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87 for i, value in enumerate(values):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 self.values[strand][i] += value
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89 progress.inc()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 progress.done()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92 for strand in self.strandNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 if strand == 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
94 strand = 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
95 for i in range(self.nbPoints + 2 * self.distance):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
96 self.values[strand][i] /= transcriptParser.getNbTranscripts() * strand
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
97
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
98
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
99 def smoothen(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
100 if self.smoothenForce == None:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101 return
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102 for strand in self.strandNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 averageValues = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 for center in range(self.distance, self.distance + self.nbPoints):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105 sum = 0.0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 nbValues = 0.0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 for i in range(center - self.smoothenForce + 1, center + self.smoothenForce):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 if i > self.distance and i < self.distance + self.nbPoints:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109 nbValues += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 sum += self.values[strand][i]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111 averageValues[center] = sum / nbValues
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112 for position in range(self.distance, self.distance + self.nbPoints):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113 self.values[strand][position] = averageValues[position]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116 def plot(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 plotter = RPlotter(self.outputFileName, self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 for strand in self.strandNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 plotter.addLine(self.values[strand])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 if self.log:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 plotter.setLog("y")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
122 plotter.setAxisLabel("x", {0: -self.distance, self.distance: "start", self.distance+self.nbPoints-1: "end", 2*self.distance+self.nbPoints-1: self.distance})
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 plotter.plot()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
127 if __name__ == "__main__":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 # parse command line
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130 description = "Get WIG Profile v1.0.1: Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
131
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
132 parser = OptionParser(description = description)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
133 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
134 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
135 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
136 parser.add_option("-p", "--nbPoints", dest="nbPoints", action="store", default=1000, type="int", help="number of points on the x-axis [compulsory] [format: int] [default: 1000]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
137 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="distance around genomic coordinates [compulsory] [format: int] [default: 0]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
138 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
139 parser.add_option("-m", "--smoothen", dest="smoothen", action="store", default=None, type="int", help="smoothen the curve [format: int] [default: None]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
140 parser.add_option("-a", "--default", dest="defaultValue", action="store", default=0.0, type="float", help="default value (when value is NA) [default: 0.0] [format: float]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
141 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
142 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
143 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
144 (options, args) = parser.parse_args()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
145
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
146 wigProfile = GetWigProfile(options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
147 wigProfile.strands = options.strands
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
148 wigProfile.inputFileName = options.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
149 wigProfile.inputFormat = options.inputFormat
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
150 wigProfile.wig = options.wig
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
151 wigProfile.nbPoints = options.nbPoints
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
152 wigProfile.distance = options.distance
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
153 wigProfile.smoothenForce = options.smoothen
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
154 wigProfile.defaultValue = options.defaultValue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
155 wigProfile.outputFileName = options.outputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
156 wigProfile.log = options.log
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
157
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
158 wigProfile.readTranscripts()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
159 wigProfile.smoothen()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
160 wigProfile.plot()