|
6
|
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 os, struct, time, shutil
|
|
|
33 from optparse import OptionParser
|
|
|
34 from commons.core.parsing.ParserChooser import ParserChooser
|
|
|
35 from commons.core.writer.Gff3Writer import Gff3Writer
|
|
|
36 from SMART.Java.Python.structure.Transcript import Transcript
|
|
|
37 from SMART.Java.Python.structure.Interval import Interval
|
|
|
38 from SMART.Java.Python.ncList.NCList import NCList
|
|
|
39 from SMART.Java.Python.ncList.ConvertToNCList import ConvertToNCList
|
|
|
40 from SMART.Java.Python.ncList.NCListParser import NCListParser
|
|
|
41 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
|
|
|
42 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
|
|
|
43 from SMART.Java.Python.ncList.NCListHandler import NCListHandler
|
|
|
44 from SMART.Java.Python.misc.Progress import Progress
|
|
|
45 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
|
|
|
46 try:
|
|
|
47 import cPickle as pickle
|
|
|
48 except:
|
|
|
49 import pickle
|
|
|
50
|
|
|
51 REFERENCE = 0
|
|
|
52 QUERY = 1
|
|
|
53 TYPES = (REFERENCE, QUERY)
|
|
|
54 TYPETOSTRING = {0: "reference", 1: "query"}
|
|
|
55
|
|
|
56 class FindOverlapsOptim(object):
|
|
|
57
|
|
|
58 def __init__(self, verbosity = 1):
|
|
|
59 self._parsers = {}
|
|
|
60 self._sortedFileNames = {}
|
|
|
61 self._outputFileName = "outputOverlaps.gff3"
|
|
|
62 self._iWriter = None
|
|
|
63 self._inputFileNames = {REFERENCE: None, QUERY: None}
|
|
|
64 self._convertedFileNames = {REFERENCE: False, QUERY: False}
|
|
|
65 self._inputFileFormats = {REFERENCE: None, QUERY: None}
|
|
|
66 self._converted = {REFERENCE: False, QUERY: False}
|
|
|
67 self._ncListHandlers = {REFERENCE: None, QUERY: None}
|
|
|
68 self._splittedFileNames = {REFERENCE: {}, QUERY: {}}
|
|
|
69 self._nbOverlappingQueries = 0
|
|
|
70 self._nbOverlaps = 0
|
|
|
71 self._nbLines = {REFERENCE: 0, QUERY: 0}
|
|
|
72 self._sorted = False
|
|
|
73 self._index = False
|
|
|
74 self._verbosity = verbosity
|
|
|
75 self._ncLists = {}
|
|
|
76 self._cursors = {}
|
|
|
77 self._nbElementsPerChromosome = {}
|
|
|
78 self._tmpDirectories = {REFERENCE: False, QUERY: False}
|
|
|
79
|
|
|
80 def close(self):
|
|
|
81 self._iWriter.close()
|
|
|
82 for fileName in (self._sortedFileNames.values()):
|
|
|
83 if os.path.exists(fileName):
|
|
|
84 os.remove(fileName)
|
|
|
85 for fileName in self._convertedFileNames.values():
|
|
|
86 if fileName:
|
|
|
87 os.remove(fileName)
|
|
|
88
|
|
|
89 def setRefFileName(self, fileName, format):
|
|
|
90 self.setFileName(fileName, format, REFERENCE)
|
|
|
91
|
|
|
92 def setQueryFileName(self, fileName, format):
|
|
|
93 self.setFileName(fileName, format, QUERY)
|
|
|
94
|
|
|
95 def setFileName(self, fileName, format, type):
|
|
|
96 self._inputFileNames[type] = fileName
|
|
|
97 self._inputFileFormats[type] = format
|
|
|
98 if format.lower() != "nclist":
|
|
|
99 self._converted[type] = True
|
|
|
100
|
|
|
101 def setOutputFileName(self, outputFileName):
|
|
|
102 self._outputFileName = outputFileName
|
|
|
103 self._iWriter = Gff3Writer(self._outputFileName)
|
|
|
104
|
|
|
105 def setSorted(self, sorted):
|
|
|
106 self._sorted = sorted
|
|
|
107
|
|
|
108 def setIndex(self, index):
|
|
|
109 self._index = index
|
|
|
110
|
|
|
111 def createNCLists(self):
|
|
|
112 startTime = time.time()
|
|
|
113 if self._verbosity > 1:
|
|
|
114 print "Building database"
|
|
|
115 self._ncLists = dict([type, {}] for type in TYPES)
|
|
|
116 self._indices = dict([type, {}] for type in TYPES)
|
|
|
117 self._cursors = dict([type, {}] for type in TYPES)
|
|
|
118 for type in TYPES:
|
|
|
119 self._ncListHandlers[type] = NCListHandler(self._verbosity-3)
|
|
|
120 if self._converted[type]:
|
|
|
121 self._convertedFileNames[type] = "%s_%d.ncl" % (os.path.splitext(self._inputFileNames[type])[0], type)
|
|
|
122 ncLists = ConvertToNCList(self._verbosity-3)
|
|
|
123 ncLists.setInputFileName(self._inputFileNames[type], self._inputFileFormats[type])
|
|
|
124 ncLists.setSorted(self._sorted)
|
|
|
125 ncLists.setOutputFileName(self._convertedFileNames[type])
|
|
|
126 if type == REFERENCE and self._index:
|
|
|
127 ncLists.setIndex(True)
|
|
|
128 ncLists.run()
|
|
|
129 self._ncListHandlers[type].setFileName(self._convertedFileNames[type])
|
|
|
130 else:
|
|
|
131 self._ncListHandlers[type].setFileName(self._inputFileNames[type])
|
|
|
132 self._ncListHandlers[type].loadData()
|
|
|
133 self._nbLines[type] = self._ncListHandlers[type].getNbElements()
|
|
|
134 self._nbElementsPerChromosome[type] = self._ncListHandlers[type].getNbElementsPerChromosome()
|
|
|
135 self._ncLists[type] = self._ncListHandlers[type].getNCLists()
|
|
|
136 for chromosome, ncList in self._ncLists[type].iteritems():
|
|
|
137 self._cursors[type][chromosome] = NCListCursor(None, ncList, 0, self._verbosity)
|
|
|
138 if type == REFERENCE and self._index:
|
|
|
139 self._indices[REFERENCE][chromosome] = ncList.getIndex()
|
|
|
140 endTime = time.time()
|
|
|
141 if self._verbosity > 1:
|
|
|
142 print "done (%.2gs)" % (endTime - startTime)
|
|
|
143
|
|
|
144 def compare(self):
|
|
|
145 nbSkips, nbMoves = 0, 0
|
|
|
146 previousChromosome = None
|
|
|
147 done = False
|
|
|
148 startTime = time.time()
|
|
|
149 progress = Progress(len(self._ncLists[QUERY].keys()), "Checking overlap", self._verbosity)
|
|
|
150 #print "query:", self._ncLists[QUERY].keys()
|
|
|
151 #print "reference:", self._ncLists[REFERENCE].keys()
|
|
|
152 for chromosome, queryNCList in self._ncLists[QUERY].iteritems():
|
|
|
153 queryParser = self._ncListHandlers[QUERY].getParser(chromosome)
|
|
|
154 queryCursor = self._cursors[QUERY][chromosome]
|
|
|
155 if chromosome != previousChromosome:
|
|
|
156 skipChromosome = False
|
|
|
157 previousChromosome = chromosome
|
|
|
158 if chromosome not in self._ncLists[REFERENCE]:
|
|
|
159 #print "out ", chromosome
|
|
|
160 continue
|
|
|
161 refNCList = self._ncLists[REFERENCE][chromosome]
|
|
|
162 refCursor = self._cursors[REFERENCE][chromosome]
|
|
|
163 #print "starting", chromosome
|
|
|
164 while True:
|
|
|
165 queryTranscript = queryCursor.getTranscript()
|
|
|
166 newRefLaddr = self.checkIndex(queryTranscript, refCursor)
|
|
|
167 #print "query is", queryTranscript
|
|
|
168 if newRefLaddr != None:
|
|
|
169 nbMoves += 1
|
|
|
170 refCursor.setLIndex(newRefLaddr)
|
|
|
171 #print "skipping to", refCursor
|
|
|
172 done = False
|
|
|
173 refCursor, done, unmatched = self.findOverlapIter(queryTranscript, refCursor, done)
|
|
|
174 #print "completed with", refCursor, done, unmatched
|
|
|
175 if refCursor.isOut():
|
|
|
176 #print "exiting 1", chromosome
|
|
|
177 break
|
|
|
178 if unmatched or not queryCursor.hasChildren():
|
|
|
179 queryCursor.moveNext()
|
|
|
180 #print "moving next to", queryCursor
|
|
|
181 nbSkips += 1
|
|
|
182 else:
|
|
|
183 queryCursor.moveDown()
|
|
|
184 #print "moving down to", queryCursor
|
|
|
185 if queryCursor.isOut():
|
|
|
186 #print "exiting 2", chromosome
|
|
|
187 break
|
|
|
188 progress.inc()
|
|
|
189 progress.done()
|
|
|
190 endTime = time.time()
|
|
|
191 self._timeSpent = endTime - startTime
|
|
|
192 if self._verbosity >= 10:
|
|
|
193 print "# skips: %d" % (nbSkips)
|
|
|
194 print "# moves: %d" % (nbMoves)
|
|
|
195
|
|
|
196 def findOverlapIter(self, queryTranscript, cursor, done):
|
|
|
197 chromosome = queryTranscript.getChromosome()
|
|
|
198 if chromosome not in self._ncLists[REFERENCE]:
|
|
|
199 return False, None
|
|
|
200 ncList = self._ncLists[REFERENCE][chromosome]
|
|
|
201 overlappingNames = {}
|
|
|
202 nextDone = False
|
|
|
203 firstOverlapLAddr = NCListCursor(cursor)
|
|
|
204 firstOverlapLAddr.setLIndex(-1)
|
|
|
205 if cursor.isOut():
|
|
|
206 return firstOverlapLAddr, False
|
|
|
207 parentCursor = NCListCursor(cursor)
|
|
|
208 parentCursor.moveUp()
|
|
|
209 firstParentAfter = False
|
|
|
210 #print "query transcript 1", queryTranscript
|
|
|
211 #print "cursor 1", cursor
|
|
|
212 #print "parent 1", parentCursor
|
|
|
213 while not parentCursor.isOut():
|
|
|
214 if self.isOverlapping(queryTranscript, parentCursor) == 0:
|
|
|
215 #print "overlap parent choice 0"
|
|
|
216 overlappingNames.update(self._extractID(parentCursor.getTranscript()))
|
|
|
217 if firstOverlapLAddr.isOut():
|
|
|
218 #print "overlap parent 2"
|
|
|
219 firstOverlapLAddr.copy(parentCursor)
|
|
|
220 nextDone = True # new
|
|
|
221 elif self.isOverlapping(queryTranscript, parentCursor) == 1:
|
|
|
222 #print "overlap parent choice 1"
|
|
|
223 firstParentAfter = NCListCursor(parentCursor)
|
|
|
224 parentCursor.moveUp()
|
|
|
225 #print "parent 2", parentCursor
|
|
|
226 if firstParentAfter:
|
|
|
227 #print "exit parent", firstParentAfter, overlappingNames
|
|
|
228 self._writeIntervalInNewGFF3(queryTranscript, overlappingNames)
|
|
|
229 return firstParentAfter, False, not overlappingNames
|
|
|
230 #This loop finds the overlaps with currentRefLAddr.#
|
|
|
231 while True:
|
|
|
232 #print "ref cursor now is", cursor
|
|
|
233 parentCursor = NCListCursor(cursor)
|
|
|
234 parentCursor.moveUp()
|
|
|
235 #In case: Query is on the right of the RefInterval and does not overlap.
|
|
|
236 overlap = self.isOverlapping(queryTranscript, cursor)
|
|
|
237 if overlap == -1:
|
|
|
238 cursor.moveNext()
|
|
|
239 #In case: Query overlaps with RefInterval.
|
|
|
240 elif overlap == 0:
|
|
|
241 #print "choice 2"
|
|
|
242 overlappingNames.update(self._extractID(cursor.getTranscript()))
|
|
|
243 if firstOverlapLAddr.compare(parentCursor):
|
|
|
244 firstOverlapLAddr.copy(cursor)
|
|
|
245 nextDone = True # new
|
|
|
246 if done:
|
|
|
247 cursor.moveNext()
|
|
|
248 else:
|
|
|
249 if not cursor.hasChildren():
|
|
|
250 cursor.moveNext()
|
|
|
251 if cursor.isOut():
|
|
|
252 #print "break 1"
|
|
|
253 break
|
|
|
254 else:
|
|
|
255 cursor.moveDown()
|
|
|
256 #In case: Query is on the left of the RefInterval and does not overlap.
|
|
|
257 else:
|
|
|
258 #print "choice 3"
|
|
|
259 if firstOverlapLAddr.isOut() or firstOverlapLAddr.compare(parentCursor):
|
|
|
260 #print "changing nfo 2"
|
|
|
261 firstOverlapLAddr.copy(cursor)
|
|
|
262 nextDone = False # new
|
|
|
263 #print "break 2"
|
|
|
264 break
|
|
|
265
|
|
|
266 done = False
|
|
|
267 if cursor.isOut():
|
|
|
268 #print "break 3"
|
|
|
269 break
|
|
|
270 self._writeIntervalInNewGFF3(queryTranscript, overlappingNames)
|
|
|
271 return firstOverlapLAddr, nextDone, not overlappingNames
|
|
|
272
|
|
|
273 def isOverlapping(self, queryTranscript, refTranscript):
|
|
|
274 if (queryTranscript.getStart() <= refTranscript.getEnd() and queryTranscript.getEnd() >= refTranscript.getStart()):
|
|
|
275 return 0
|
|
|
276 if queryTranscript.getEnd() < refTranscript.getStart():
|
|
|
277 return 1
|
|
|
278 return -1
|
|
|
279
|
|
|
280 def checkIndex(self, transcript, cursor):
|
|
|
281 if not self._index:
|
|
|
282 return None
|
|
|
283 chromosome = transcript.getChromosome()
|
|
|
284 nextLIndex = self._indices[REFERENCE][chromosome].getIndex(transcript)
|
|
|
285 if nextLIndex == None:
|
|
|
286 return None
|
|
|
287 ncList = self._ncLists[REFERENCE][chromosome]
|
|
|
288 nextGffAddress = ncList.getRefGffAddr(nextLIndex)
|
|
|
289 thisGffAddress = cursor.getGffAddress()
|
|
|
290 if nextGffAddress > thisGffAddress:
|
|
|
291 return nextLIndex
|
|
|
292 return None
|
|
|
293
|
|
|
294 def _writeIntervalInNewGFF3(self, transcript, names):
|
|
|
295 nbOverlaps = 0
|
|
|
296 for cpt in names.values():
|
|
|
297 nbOverlaps += cpt
|
|
|
298 if not names:
|
|
|
299 return
|
|
|
300 transcript.setTagValue("overlapsWith", "--".join(sorted(names.keys())))
|
|
|
301 transcript.setTagValue("nbOverlaps", nbOverlaps)
|
|
|
302 self._iWriter.addTranscript(transcript)
|
|
|
303 self._iWriter.write()
|
|
|
304 self._nbOverlappingQueries += 1
|
|
|
305 self._nbOverlaps += nbOverlaps
|
|
|
306
|
|
|
307 def _extractID(self, transcript):
|
|
|
308 nbElements = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
|
|
|
309 id = transcript.getTagValue("ID") if "ID" in transcript.getTagNames() else transcript.getUniqueName()
|
|
|
310 return {id: nbElements}
|
|
|
311
|
|
|
312 def run(self):
|
|
|
313 self.createNCLists()
|
|
|
314 self.compare()
|
|
|
315 self.close()
|
|
|
316 if self._verbosity > 0:
|
|
|
317 print "# queries: %d" % (self._nbLines[QUERY])
|
|
|
318 print "# refs: %d" % (self._nbLines[REFERENCE])
|
|
|
319 print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps)
|
|
|
320 print "time: %.2gs" % (self._timeSpent)
|
|
|
321
|
|
|
322
|
|
|
323 if __name__ == "__main__":
|
|
|
324 description = "Find Overlaps Optim v1.0.0: Finds overlaps with several query intervals. [Category: Data Comparison]"
|
|
|
325
|
|
|
326 parser = OptionParser(description = description)
|
|
|
327 parser.add_option("-i", "--query", dest="inputQueryFileName", action="store", type="string", help="query input file [compulsory] [format: file in transcript or other format given by -f]")
|
|
|
328 parser.add_option("-f", "--queryFormat", dest="queryFormat", action="store", type="string", help="format of previous file (possibly in NCL format) [compulsory] [format: transcript or other file format]")
|
|
|
329 parser.add_option("-j", "--ref", dest="inputRefFileName", action="store", type="string", help="reference input file [compulsory] [format: file in transcript or other format given by -g]")
|
|
|
330 parser.add_option("-g", "--refFormat", dest="refFormat", action="store", type="string", help="format of previous file (possibly in NCL format) [compulsory] [format: transcript or other file format]")
|
|
|
331 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
|
|
|
332 parser.add_option("-d", "--index", dest="index", action="store_true", default=False, help="add an index to the reference file (faster but more memory) [format: boolean] [default: False]")
|
|
|
333 parser.add_option("-s", "--sorted", dest="sorted", action="store_true", default=False, help="input files are already sorted [format: boolean] [default: False]")
|
|
|
334 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]")
|
|
|
335 (options, args) = parser.parse_args()
|
|
|
336
|
|
|
337 iFOO = FindOverlapsOptim(options.verbosity)
|
|
|
338 iFOO.setRefFileName(options.inputRefFileName, options.refFormat)
|
|
|
339 iFOO.setQueryFileName(options.inputQueryFileName, options.queryFormat)
|
|
|
340 iFOO.setOutputFileName(options.outputFileName)
|
|
|
341 iFOO.setIndex(options.index)
|
|
|
342 iFOO.setSorted(options.sorted)
|
|
|
343 iFOO.run()
|
