Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervals.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
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 import os, struct, time
33 from optparse import OptionParser
34 from commons.core.parsing.ParserChooser import ParserChooser
35 from SMART.Java.Python.structure.Transcript import Transcript
36 from SMART.Java.Python.ncList.NCList import NCList
37 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
38 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
39 from SMART.Java.Python.ncList.FileSorter import FileSorter
40 from SMART.Java.Python.misc.Progress import Progress
41 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
42 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
43 from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval
44
45 REFERENCE = 0
46 QUERY = 1
47 TYPETOSTRING = {0: "reference", 1: "query"}
48
49 class FindOverlapsWithSeveralIntervals(object):
50
51 def __init__(self, verbosity = 1):
52 self._parsers = {}
53 self._outputFileName = "outputOverlaps.gff3"
54 self._iWriter = None
55 self._nbLines = {REFERENCE: 0, QUERY: 0}
56 self._verbosity = verbosity
57 self._ncLists = {}
58 self._sortedRefFileNames = None
59 self._transQueryFileName = None
60 self._cursors = {}
61 self._iFowoi = FindOverlapsWithOneInterval(self._verbosity)
62
63 def __del__(self):
64 self.close()
65 for fileName in (self._sortedRefFileNames, self._transQueryFileName):
66 if os.path.exists(fileName):
67 os.remove(fileName)
68
69 def close(self):
70 self._iFowoi.close()
71
72 def setRefFileName(self, fileName, format):
73 self.setFileName(fileName, format, REFERENCE)
74 self._sortedRefFileNames = "%s_ref_sorted.pkl" % (os.path.splitext(fileName)[0])
75
76 def setQueryFileName(self, fileName, format):
77 self.setFileName(fileName, format, QUERY)
78 self._transQueryFileName = "%s_query_trans.pkl" % (os.path.splitext(fileName)[0])
79
80 def setFileName(self, fileName, format, type):
81 chooser = ParserChooser(self._verbosity)
82 chooser.findFormat(format)
83 self._parsers[type] = chooser.getParser(fileName)
84
85 def setOutputFileName(self, outputFileName):
86 self._iFowoi.setOutputFileName(outputFileName)
87
88 def _sortRefFile(self):
89 fs = FileSorter(self._parsers[REFERENCE], self._verbosity-4)
90 fs.perChromosome(True)
91 fs.setOutputFileName(self._sortedRefFileNames)
92 fs.sort()
93 self._nbLines[REFERENCE] = fs.getNbElements()
94 self._nbRefLinesPerChromosome = fs.getNbElementsPerChromosome()
95 self._splittedFileNames = fs.getOutputFileNames()
96
97 def _translateQueryFile(self):
98 pickler = NCListFilePickle(self._transQueryFileName, self._verbosity)
99 progress = UnlimitedProgress(1000, "Translating query data", self._verbosity-4)
100 cpt = 0
101 for queryTranscript in self._parsers[QUERY].getIterator():
102 pickler.addTranscript(queryTranscript)
103 progress.inc()
104 cpt += 1
105 progress.done()
106 self._nbLines[QUERY] = cpt
107 self._parsers[QUERY] = NCListFileUnpickle(self._transQueryFileName, self._verbosity)
108
109 def prepareIntermediateFiles(self):
110 self._sortRefFile()
111 self._translateQueryFile()
112
113 def createNCLists(self):
114 self._ncLists = {}
115 self._indices = {}
116 self._cursors = {}
117 for chromosome, fileName in self._splittedFileNames.iteritems():
118 if self._verbosity > 3:
119 print " chromosome %s" % (chromosome)
120 ncList = NCList(self._verbosity)
121 ncList.createIndex(True)
122 ncList.setChromosome(chromosome)
123 ncList.setFileName(fileName)
124 ncList.setNbElements(self._nbRefLinesPerChromosome[chromosome])
125 ncList.buildLists()
126 self._ncLists[chromosome] = ncList
127 cursor = NCListCursor(None, ncList, 0, self._verbosity)
128 self._cursors[chromosome] = cursor
129 self._indices[chromosome] = ncList.getIndex()
130 endTime = time.time()
131
132 def compare(self):
133 progress = Progress(self._nbLines[QUERY], "Comparing data", self._verbosity-3)
134 startTime = time.time()
135 for cpt, queryTranscript in enumerate(self._parsers[QUERY].getIterator()):
136 chromosome = queryTranscript.getChromosome()
137 if chromosome not in self._ncLists:
138 continue
139 self._iFowoi.setNCList(self._ncLists[chromosome], self._indices[chromosome])
140 self._iFowoi.setTranscript(queryTranscript)
141 self._iFowoi.compare()
142 self._iFowoi.dumpWriter()
143 progress.inc()
144 progress.done()
145 endTime = time.time()
146 self._timeSpent = endTime - startTime
147
148 def run(self):
149 startTime = time.time()
150 if self._verbosity > 2:
151 print "Creating NC-list..."
152 self.prepareIntermediateFiles()
153 self.createNCLists()
154 endTime = time.time()
155 if self._verbosity > 2:
156 print " ...done (%.2gs)" % (endTime - startTime)
157 self.compare()
158 self.close()
159 if self._verbosity > 0:
160 print "# queries: %d" % (self._nbLines[QUERY])
161 print "# refs: %d" % (self._nbLines[REFERENCE])
162 print "# written: %d (%d overlaps)" % (self._iFowoi._nbWritten, self._iFowoi._nbOverlaps)
163 print "time: %.2gs" % (self._timeSpent)
164
165
166 if __name__ == "__main__":
167 description = "FindOverlaps With Several Intervals v1.0.0: Finds overlaps with several query intervals. [Category: Data comparison]"
168
169 parser = OptionParser(description = description)
170 parser.add_option("-i", "--query", dest="inputQueryFileName", action="store", type="string", help="Query input file [compulsory] [format: file in transcript format given by -f]")
171 parser.add_option("-f", "--queryFormat", dest="queryFormat", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
172 parser.add_option("-j", "--ref", dest="inputRefFileName", action="store", type="string", help="Reference input file [compulsory] [format: file in transcript format given by -g]")
173 parser.add_option("-g", "--refFormat", dest="refFormat", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
174 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="Output file [compulsory] [format: output file in GFF3 format]")
175 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]")
176 (options, args) = parser.parse_args()
177
178 iFWSI = FindOverlapsWithSeveralIntervals(options.verbosity)
179 iFWSI.setRefFileName(options.inputRefFileName, options.refFormat)
180 iFWSI.setQueryFileName(options.inputQueryFileName, options.queryFormat)
181 iFWSI.setOutputFileName(options.outputFileName)
182 iFWSI.run()