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comparison smart_toolShed/SMART/Java/Python/GetUpDownStream.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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-1:000000000000 0:e0f8dcca02ed
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2012
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 import os
32 from optparse import OptionParser, OptionGroup
33 from commons.core.parsing.ParserChooser import ParserChooser
34 from commons.core.writer.Gff3Writer import Gff3Writer
35 from SMART.Java.Python.structure.Transcript import Transcript
36 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
37 from SMART.Java.Python.ncList.FileSorter import FileSorter
38 from SMART.Java.Python.misc.Progress import Progress
39 from SMART.Java.Python.misc import Utils
40
41
42 class GetUpDownStream(object):
43
44 def __init__(self, verbosity = 0):
45 self.verbosity = verbosity
46 self.inputReader = None
47 self.outputWriter = None
48 self.nbRead = 0
49 self.nbWritten = 0
50 self.nbMerges = 0
51 self.splittedFileNames = {}
52
53 def __del__(self):
54 for fileName in self.splittedFileNames.values():
55 os.remove(fileName)
56
57 def setInputFile(self, fileName, format):
58 parserChooser = ParserChooser(self.verbosity)
59 parserChooser.findFormat(format, "transcript")
60 self.parser = parserChooser.getParser(fileName)
61 self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
62
63 def setOutputFile(self, fileName):
64 self.outputWriter = Gff3Writer(fileName, self.verbosity)
65
66 def setDistances(self, up, down):
67 self.upDistance = up
68 self.downDistance = down
69
70 def _sortFile(self):
71 fs = FileSorter(self.parser, self.verbosity-4)
72 fs.perChromosome(True)
73 fs.setOutputFileName(self.sortedFileName)
74 fs.sort()
75 self.splittedFileNames = fs.getOutputFileNames()
76 self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
77 self.nbRead = fs.getNbElements()
78
79 def _write(self, start, end, reference, after):
80 if start > end:
81 return
82 transcript = Transcript()
83 transcript.setChromosome(reference.getChromosome())
84 transcript.setStart(start)
85 transcript.setEnd(end)
86 transcript.setDirection("+")
87 transcript.setName("%s_%s" % ("up" if Utils.xor(reference.getDirection() == 1, after) else "down", reference.getName()))
88 self.outputWriter.addTranscript(transcript)
89
90 def _getFlanking(self, chromosome):
91 progress = Progress(self.nbElementsPerChromosome[chromosome], "Analyzing chromosome %s" % (chromosome), self.verbosity)
92 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
93 previous = None
94 for transcript in parser.getIterator():
95 progress.inc()
96 transcript.removeExons()
97 if previous == None:
98 distance = self.upDistance if transcript.getDirection() == 1 else self.downDistance
99 start = max(1, transcript.getStart() - distance)
100 self._write(start, transcript.getStart()-1, transcript, False)
101 previous = transcript
102 continue
103 if previous.include(transcript):
104 continue
105 if transcript.overlapWith(previous):
106 previous = transcript
107 continue
108 distancePrevious = self.downDistance if previous.getDirection() == 1 else self.upDistance
109 distanceCurrent = self.upDistance if transcript.getDirection() == 1 else self.downDistance
110 distance = transcript.getDistance(previous)
111 if distancePrevious + distanceCurrent == 0:
112 previous = transcript
113 continue
114 if distance >= distancePrevious + distanceCurrent:
115 endPrevious = previous.getEnd() + distancePrevious
116 startCurrent = transcript.getStart() - distanceCurrent
117 else:
118 middle = previous.getEnd() + int((distance-1) * float(distancePrevious) / (distancePrevious + distanceCurrent))
119 endPrevious = middle
120 startCurrent = middle+1
121 self._write(previous.getEnd() + 1, endPrevious, previous, True)
122 self._write(startCurrent, transcript.getStart() - 1, transcript, False)
123 previous = transcript
124 distance = self.downDistance if previous.getDirection() == 1 else self.upDistance
125 self._write(previous.getEnd() + 1, previous.getEnd() + distance, previous, True)
126 progress.done()
127
128 def run(self):
129 self._sortFile()
130 for chromosome in sorted(self.nbElementsPerChromosome.keys()):
131 self._getFlanking(chromosome)
132 self.outputWriter.close()
133
134 if __name__ == "__main__":
135
136 # parse command line
137 description = "Get Up and Down Stream v1.0.0: Get the flanking regions of an annotation. [Category: Data Modification]"
138
139 parser = OptionParser(description = description)
140 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
141 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the file [compulsory] [format: mapping file format]")
142 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
143 parser.add_option("-u", "--up", dest="up", action="store", default=0, type="int", help="the upstream distance [format: int]")
144 parser.add_option("-d", "--down", dest="down", action="store", default=0, type="int", help="the downstream distance [format: int]")
145 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
146 (options, args) = parser.parse_args()
147
148 guds = GetUpDownStream(options.verbosity)
149 guds.setInputFile(options.inputFileName, options.format)
150 guds.setOutputFile(options.outputFileName)
151 guds.setDistances(options.up, options.down)
152 guds.run()