annotate SMART/Java/Python/clusterize.py @ 71:d96f6c9a39e0 draft default tip

Removed pyc 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 from commons.core.writer.WriterChooser import WriterChooser
32 """Clusterize a set of transcripts"""
33 
34 import os, os.path, random
35 from optparse import OptionParser
36 from heapq import heappush, heappop
37 from commons.core.parsing.ParserChooser import ParserChooser
38 from commons.core.writer.Gff3Writer import Gff3Writer
39 from SMART.Java.Python.structure.Transcript import Transcript
40 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
41 from SMART.Java.Python.ncList.FileSorter import FileSorter
42 from SMART.Java.Python.misc.Progress import Progress
43 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
44 
45 class Clusterize(object):
46 
47 	def __init__(self, verbosity):
48 		self.parsers           = {}
49 		self.sortedFileNames   = {}
50 		self.normalize         = False
51 		self.presorted         = False
52 		self.distance          = 1
53 		self.collinear         = False
54 		self.nbWritten         = 0
55 		self.nbMerges          = 0
56 		self.verbosity         = verbosity
57 		self.splittedFileNames = {}
58 		self.chromosomes       = set()
59 
60 	def __del__(self):
61 		for fileName1 in self.splittedFileNames:
62 			for fileName2 in self.splittedFileNames[fileName1].values():
63 				os.remove(fileName2)
64 
65 	def setInputFiles(self, fileNames, format):
66 		parserChooser = ParserChooser(self.verbosity)
67 		parserChooser.findFormat(format)
68 		for fileName in fileNames:
69 			self.parsers[fileName] = parserChooser.getParser(fileName)
70 			self.sortedFileNames[fileName] = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000))
71 			if "SMARTTMPPATH" in os.environ:
72 				self.sortedFileNames[fileName] = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileNames[fileName]))
73 
74 	def setOutputFileName(self, fileName, format="gff3", title="S-MART", feature="transcript", featurePart="exon"):
75 		writerChooser = WriterChooser()
76 		writerChooser.findFormat(format)
77 		self.writer = writerChooser.getWriter(fileName)
78 		self.writer.setTitle(title)
79 		self.writer.setFeature(feature)
80 		self.writer.setFeaturePart(featurePart)
81 
82 	def setDistance(self, distance):
83 		self.distance = distance
84 
85 	def setColinear(self, collinear):
86 		self.collinear = collinear
87 
88 	def setNormalize(self, normalize):
89 		self.normalize = normalize
90 		
91 	def setPresorted(self, presorted):
92 		self.presorted = presorted
93 
94 	def _sortFiles(self):
95 		if self.presorted:
96 			return
97 		for fileName, parser in self.parsers.iteritems():
98 			fs = FileSorter(parser, self.verbosity-4)
99 			fs.perChromosome(True)
00 			fs.setPresorted(self.presorted)
01 			fs.setOutputFileName(self.sortedFileNames[fileName])
02 			fs.sort()
03 			self.splittedFileNames[fileName] = fs.getOutputFileNames()
04 			self.chromosomes.update(self.splittedFileNames[fileName].keys())
05 		
06 	def _iterate(self):
07 		progress = UnlimitedProgress(10000, "Reading input file", self.verbosity)
08 		parsersSets = []
09 		self.nbElements = 0
10 		if self.chromosomes:
11 			for chromosome in self.chromosomes:
12 				parsersSets.append([NCListFileUnpickle(self.splittedFileNames[fileName][chromosome]) for fileName in self.splittedFileNames if chromosome in self.splittedFileNames[fileName]])
13 		else:
14 			parsersSets.append(self.parsers.values())
15 		for parsers in parsersSets:
16 			transcripts = []
17 			heap        = []
18 			for parser in parsers:
19 				iterator = parser.getIterator()
20 				for transcript in iterator:
21 					if transcript.__class__.__name__ == "Mapping":
22 						transcript = transcript.getTranscript()
23 					heappush(heap, (transcript.getChromosome(), transcript.getStart(), -transcript.getEnd(), transcript, iterator))
24 					break
25 			while heap:
26 				chromosome, start, end, newTranscript, iterator = heappop(heap)
27 				for transcript in iterator:
28 					if transcript.__class__.__name__ == "Mapping":
29 						transcript = transcript.getTranscript()
30 					heappush(heap, (transcript.getChromosome(), transcript.getStart(), -transcript.getEnd(), transcript, iterator))
31 					break
32 				newTranscripts = []
33 				if newTranscript.__class__.__name__ == "Mapping":
34 					newTranscript = newTranscript.getTranscript()
35 				for oldTranscript in transcripts:
36 					if self._checkOverlap(newTranscript, oldTranscript):
37 						self._merge(newTranscript, oldTranscript)
38 					elif self._checkPassed(newTranscript, oldTranscript):
39 						self._write(oldTranscript)
40 					else:
41 						newTranscripts.append(oldTranscript)
42 				newTranscripts.append(newTranscript)
43 				transcripts = newTranscripts
44 				self.nbElements += 1
45 				progress.inc()
46 			for transcript in transcripts:
47 				self._write(transcript)
48 		progress.done()
49 
50 	def _merge(self, transcript1, transcript2):
51 		self.nbMerges += 1
52 		transcript2.setDirection(transcript1.getDirection())
53 		transcript1.merge(transcript2)
54 
55 	def _write(self, transcript):
56 		self.nbWritten += 1
57 		self.writer.addTranscript(transcript)
58 
59 	def _checkOverlap(self, transcript1, transcript2):
60 		if transcript1.getChromosome() != transcript2.getChromosome():
61 			return False
62 		if self.collinear and transcript1.getDirection() != transcript2.getDirection():
63 			return False
64 		if transcript1.getDistance(transcript2) > self.distance:
65 			return False
66 		return True
67 
68 	def _checkPassed(self, transcript1, transcript2):
69 		return ((transcript1.getChromosome() != transcript2.getChromosome()) or (transcript1.getDistance(transcript2) > self.distance))
70 
71 	def run(self):
72 		self._sortFiles()
73 		self._iterate()
74 		self.writer.close()
75 		if self.verbosity > 0:
76 			print "# input:   %d" % (self.nbElements)
77 			print "# written: %d (%d%% overlaps)" % (self.nbWritten, 0 if (self.nbElements == 0) else ((float(self.nbWritten) / self.nbElements) * 100))
78 			print "# merges:  %d" % (self.nbMerges)
79 		
80 
81 if __name__ == "__main__":
82 	description = "Clusterize v1.0.3: clusterize the data which overlap. [Category: Merge]"
83 
84 	parser = OptionParser(description = description)
85 	parser.add_option("-i", "--inputs",       dest="inputFileNames", action="store",				     type="string", help="input files (separated by commas) [compulsory] [format: string]")
86 	parser.add_option("-f", "--format",       dest="format",		 action="store",				     type="string", help="format of file [format: transcript file format]")
87 	parser.add_option("-o", "--output",       dest="outputFileName", action="store",				     type="string", help="output file [compulsory] [format: output file in transcript format given by -u]")
88 	parser.add_option("-u", "--outputFormat", dest="outputFormat",   action="store",      default="gff",		        type="string", help="output file format [format: transcript file format]")
89 	parser.add_option("-c", "--collinear",    dest="collinear",      action="store_true", default=False,				help="merge collinear transcripts only [format: bool] [default: false]")
90 	parser.add_option("-d", "--distance",     dest="distance",       action="store",      default=0,     type="int",    help="max. distance between two transcripts to be merged [format: int] [default: 0]")
91 	parser.add_option("-n", "--normalize",    dest="normalize",      action="store_true", default=False,				help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
92 	parser.add_option("-s", "--sorted",       dest="sorted",		 action="store_true", default=False,				help="input is already sorted [format: bool] [default: false]")
93 	parser.add_option("-v", "--verbosity",    dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int] [default: 1]")
94 	(options, args) = parser.parse_args()
95 
96 	c = Clusterize(options.verbosity)
97 	c.setInputFiles(options.inputFileNames.split(","), options.format)
98 	c.setOutputFileName(options.outputFileName, options.outputFormat)
99 	c.setColinear(options.collinear)
00 	c.setDistance(options.distance)
01 	c.setNormalize(options.normalize)
02 	c.setPresorted(options.sorted)
03 	c.run()