annotate SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervals.py @ 52:418794381650

Deleted selected files

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)
00         cpt      = 0
01         for queryTranscript in self._parsers[QUERY].getIterator():
02             pickler.addTranscript(queryTranscript)
03             progress.inc()
04             cpt += 1
05         progress.done()
06         self._nbLines[QUERY] = cpt
07         self._parsers[QUERY] = NCListFileUnpickle(self._transQueryFileName, self._verbosity)
08             
09     def prepareIntermediateFiles(self):
10         self._sortRefFile()
11         self._translateQueryFile()
12 
13     def createNCLists(self):
14         self._ncLists = {}
15         self._indices = {}
16         self._cursors = {}
17         for chromosome, fileName in self._splittedFileNames.iteritems():
18             if self._verbosity > 3:
19                 print "  chromosome %s" % (chromosome)
20             ncList = NCList(self._verbosity)
21             ncList.createIndex(True)
22             ncList.setChromosome(chromosome)
23             ncList.setFileName(fileName)
24             ncList.setNbElements(self._nbRefLinesPerChromosome[chromosome])
25             ncList.buildLists()
26             self._ncLists[chromosome] = ncList
27             cursor = NCListCursor(None, ncList, 0, self._verbosity)
28             self._cursors[chromosome] = cursor
29             self._indices[chromosome] = ncList.getIndex()
30         endTime = time.time()
31 
32     def compare(self):
33         progress = Progress(self._nbLines[QUERY], "Comparing data", self._verbosity-3)
34         startTime = time.time()
35         for cpt, queryTranscript in enumerate(self._parsers[QUERY].getIterator()):
36             chromosome = queryTranscript.getChromosome()
37             if chromosome not in self._ncLists:
38                 continue
39             self._iFowoi.setNCList(self._ncLists[chromosome], self._indices[chromosome])
40             self._iFowoi.setTranscript(queryTranscript)
41             self._iFowoi.compare()
42             self._iFowoi.dumpWriter()
43             progress.inc()
44         progress.done()
45         endTime = time.time()
46         self._timeSpent = endTime - startTime
47 
48     def run(self):
49         startTime = time.time()
50         if self._verbosity > 2:
51             print "Creating NC-list..."
52         self.prepareIntermediateFiles()
53         self.createNCLists()
54         endTime = time.time()
55         if self._verbosity > 2:
56             print "    ...done (%.2gs)" % (endTime - startTime)
57         self.compare()
58         self.close()
59         if self._verbosity > 0:
60             print "# queries: %d" % (self._nbLines[QUERY])
61             print "# refs:    %d" % (self._nbLines[REFERENCE])
62             print "# written: %d (%d overlaps)" % (self._iFowoi._nbWritten, self._iFowoi._nbOverlaps)
63             print "time:      %.2gs" % (self._timeSpent)
64 
65 
66 if __name__ == "__main__":
67     description = "FindOverlaps With Several Intervals v1.0.0: Finds overlaps with several query intervals. [Category: Data comparison]"
68 
69     parser = OptionParser(description = description)
70     parser.add_option("-i", "--query",       dest="inputQueryFileName", action="store",            type="string",  help="Query input file [compulsory] [format: file in transcript format given by -f]")
71     parser.add_option("-f", "--queryFormat", dest="queryFormat",        action="store",            type="string",  help="format of previous file [compulsory] [format: transcript file format]")
72     parser.add_option("-j", "--ref",         dest="inputRefFileName",   action="store",            type="string",  help="Reference input file [compulsory] [format: file in transcript format given by -g]")
73     parser.add_option("-g", "--refFormat",   dest="refFormat",          action="store",            type="string",  help="format of previous file [compulsory] [format: transcript file format]")
74     parser.add_option("-o", "--output",      dest="outputFileName",     action="store",            type="string",  help="Output file [compulsory] [format: output file in GFF3 format]")
75     parser.add_option("-v", "--verbosity",   dest="verbosity",          action="store", default=1, type="int",     help="Trace level [format: int] [default: 1]")
76     (options, args) = parser.parse_args()
77     
78     iFWSI = FindOverlapsWithSeveralIntervals(options.verbosity)
79     iFWSI.setRefFileName(options.inputRefFileName, options.refFormat)
80     iFWSI.setQueryFileName(options.inputQueryFileName, options.queryFormat)
81     iFWSI.setOutputFileName(options.outputFileName)
82     iFWSI.run()