annotate SMART/Java/Python/ncList/ConvertToNCList.py @ 24:452e051f6562

Deleted selected files

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 
32 import random, os, time, shutil
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.structure.Interval import Interval
37 from SMART.Java.Python.ncList.NCList import NCList
38 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
40 from SMART.Java.Python.ncList.FileSorter import FileSorter
41 from SMART.Java.Python.ncList.NCListMerger import NCListMerger
42 from SMART.Java.Python.misc.Progress import Progress
43 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
44 try:
45    import cPickle as pickle
46 except:
47    import pickle
48 
49 class ConvertToNCList(object):
50 	
51 	def __init__(self, verbosity = 1):
52 		self._parsers				  = {}
53 		self._sortedFileNames		  = {}
54 		self._inputFileName		      = None
55 		self._outputFileName		  = None
56 		self._index				      = False
57 		self._ncLists				  = {}
58 		self._splittedFileNames	      = {}
59 		self._nbElements			  = 0
60 		self._nbElementsPerChromosome = {}
61 		self._randomNumber			  = random.randint(0, 10000)
62 		self._sorted                  = False
63 		self._verbosity			      = verbosity
64 		
65 	def setInputFileName(self, fileName, format):
66 		self._inputFileName = fileName
67 		chooser = ParserChooser(self._verbosity)
68 		chooser.findFormat(format)
69 		self._parser = chooser.getParser(fileName)
70 		
71 	def setOutputFileName(self, fileName):
72 		self._outputFileName = fileName
73 		fileNameNoExtension  = os.path.splitext(fileName)[0]
74 		baseName			 = "%s_%d" % (fileNameNoExtension, self._randomNumber)
75 		self._directory	     = "%s_files" % (baseName)
76 		if not os.path.exists(self._directory):
77 			os.makedirs(self._directory)
78 		self._sortedFileNames = os.path.join(self._directory, baseName)
79 
80 	def setIndex(self, boolean):
81 		self._index = boolean
82 
83 	def setSorted(self, boolean):
84 		self._sorted = boolean
85 
86 	def sortFile(self):
87 		if self._verbosity > 2:
88 			print "%s file %s..." % ("Rewriting" if self._sorted else "Sorting", self._inputFileName)
89 		startTime = time.time()
90 		fs = FileSorter(self._parser, self._verbosity-4)
91 		fs.setPresorted(self._sorted)
92 		fs.perChromosome(True)
93 		fs.setOutputFileName(self._sortedFileNames)
94 		fs.sort()
95 		self._splittedFileNames	      = fs.getOutputFileNames()
96 		self._nbElementsPerChromosome = fs.getNbElementsPerChromosome()
97 		self._nbElements			  = fs.getNbElements()
98 		endTime = time.time()
99 		if self._verbosity > 2:
00 			print "	...done (%ds)" % (endTime - startTime)
01 			
02 	def createNCLists(self):
03 		self._ncLists = {}
04 		if self._verbosity > 2:
05 			print "Creating NC-list for %s..." % (self._inputFileName)
06 		startTime = time.time()
07 		for chromosome, fileName in self._splittedFileNames.iteritems():
08 			if self._verbosity > 3:
09 				print "  chromosome %s" % (chromosome)
10 			ncList = NCList(self._verbosity)
11 			if self._index:
12 				ncList.createIndex(True)
13 			ncList.setChromosome(chromosome)
14 			ncList.setFileName(fileName)
15 			ncList.setNbElements(self._nbElementsPerChromosome[chromosome])
16 			ncList.buildLists()
17 			self._ncLists[chromosome] = ncList
18 		endTime = time.time()
19 		if self._verbosity > 2:
20 			print "	...done (%ds)" % (endTime - startTime)
21 
22 	def writeOutputFile(self):
23 		merger = NCListMerger(self._verbosity)
24 		merger.setFileName(self._outputFileName)
25 		merger.addIndex(self._index)
26 		merger.setNCLists(self._ncLists)
27 		merger.merge()
28 
29 	def cleanFiles(self):
30 		shutil.rmtree(self._directory)
31 
32 	def run(self):
33 		self.sortFile()
34 		self.createNCLists()
35 		self.writeOutputFile()
36 		self.cleanFiles()
37 
38 	def getSortedFileNames(self):
39 		return self._splittedFileNames
40 
41 	def getNbElements(self):
42 		return self._nbElements
43 
44 	def getNbElementsPerChromosome(self):
45 		return self._nbElementsPerChromosome
46 
47 	def getNCLists(self):
48 		return self._ncLists
49 
50 	def getTmpDirectory(self):
51 		return self._directory
52 
53 
54 if __name__ == "__main__":
55 	description = "Convert To NC-List v1.0.0: Convert a mapping or transcript file into a NC-List. [Category: NC-List]"
56 
57 	parser = OptionParser(description = description)
58 	parser.add_option("-i", "--input",	   dest="inputFileName",  action="store",					  type="string",  help="Query input file [compulsory] [format: file in transcript format given by -f]")
59 	parser.add_option("-f", "--format",	   dest="format",		  action="store",					  type="string",  help="format of previous file [compulsory] [format: transcript file format]")
60 	parser.add_option("-d", "--index",	   dest="index",		  action="store_true", default=False,				  help="create an index [default: false] [format: boolean]")
61 	parser.add_option("-o", "--output",	   dest="outputFileName", action="store",					  type="string",  help="Output file [compulsory] [format: output file in NCList format]")
62 	parser.add_option("-s", "--sorted",	   dest="sorted",	      action="store_true", default=False,	              help="input file is already sorted [format: boolean] [default: False]")
63 	parser.add_option("-v", "--verbosity", dest="verbosity",	  action="store",	   default=1,	  type="int",	  help="Trace level [format: int] [default: 1]")
64 	(options, args) = parser.parse_args()
65 	
66 	ctncl = ConvertToNCList(options.verbosity)
67 	ctncl.setInputFileName(options.inputFileName, options.format)
68 	ctncl.setOutputFileName(options.outputFileName)
69 	ctncl.setIndex(options.index)
70 	ctncl.setSorted(options.sorted)
71 	ctncl.run()
72