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comparison TEisotools-1.0/commons/core/coord/AlignUtils.py @ 6:20ec0d14798e draft

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date Wed, 20 Jul 2016 05:00:24 -0400
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5:4093a2fb58be 6:20ec0d14798e
1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
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
33 import sys
34 import shutil
35 from commons.core.coord.Align import Align
36
37
38 ## Static methods manipulating Align instances
39 #
40 class AlignUtils( object ):
41
42 ## Return a list with Align instances from the given file
43 #
44 # @param inFile name of a file in the Align format
45 #
46 def getAlignListFromFile( inFile ):
47 lAlignInstances = []
48 inFileHandler = open( inFile, "r" )
49 while True:
50 line = inFileHandler.readline()
51 if line == "":
52 break
53 a = Align()
54 a.setFromString( line )
55 lAlignInstances.append( a )
56 inFileHandler.close()
57 return lAlignInstances
58
59 getAlignListFromFile = staticmethod( getAlignListFromFile )
60
61
62 ## Return a list with all the scores
63 #
64 # @param lAlignInstances: list of Align instances
65 #
66 def getListOfScores( lAlignInstances ):
67 lScores = []
68 for iAlign in lAlignInstances:
69 lScores.append( iAlign.score )
70 return lScores
71
72 getListOfScores = staticmethod( getListOfScores )
73
74
75 ## Return a list with all the scores from the given file
76 #
77 # @param inFile name of a file in the Align format
78 #
79 def getScoreListFromFile(inFile):
80 lScores = []
81 append = lScores.append
82 with open(inFile, "r") as inFileHandler:
83 line = inFileHandler.readline()
84 while line:
85 if line != "\n":
86 append(int(line.split('\t')[7]))
87 line = inFileHandler.readline()
88 return lScores
89
90 getScoreListFromFile = staticmethod( getScoreListFromFile )
91
92
93 ## for each line of a given Align file, write the coordinates on the query and the subject as two distinct lines in a Map file
94 #
95 # @param alignFile: name of the input Align file
96 # @param mapFile: name of the output Map file
97 #
98 def convertAlignFileIntoMapFileWithQueriesAndSubjects( alignFile, mapFile ):
99 alignFileHandler = open( alignFile, "r" )
100 mapFileHandler = open( mapFile, "w" )
101 iAlign = Align()
102 while True:
103 line = alignFileHandler.readline()
104 if line == "":
105 break
106 iAlign.setFromString( line )
107 iMapQ, iMapS = iAlign.getMapsOfQueryAndSubject()
108 iMapQ.write( mapFileHandler )
109 iMapS.write( mapFileHandler )
110 alignFileHandler.close()
111 mapFileHandler.close()
112
113 convertAlignFileIntoMapFileWithQueriesAndSubjects = staticmethod( convertAlignFileIntoMapFileWithQueriesAndSubjects )
114
115
116 ## for each line of a given Align file, write the coordinates of the subject on the query as one line in a Map file
117 #
118 # @param alignFile: name of the input Align file
119 # @param mapFile: name of the output Map file
120 #
121 def convertAlignFileIntoMapFileWithSubjectsOnQueries( alignFile, mapFile ):
122 alignFileHandler = open( alignFile, "r" )
123 mapFileHandler = open( mapFile, "w" )
124 iAlign = Align()
125 while True:
126 line = alignFileHandler.readline()
127 if line == "":
128 break
129 iAlign.setFromString( line )
130 iMapQ = iAlign.getSubjectAsMapOfQuery()
131 iMapQ.write( mapFileHandler )
132 alignFileHandler.close()
133 mapFileHandler.close()
134
135 convertAlignFileIntoMapFileWithSubjectsOnQueries = staticmethod( convertAlignFileIntoMapFileWithSubjectsOnQueries )
136
137
138 ## return a list of Align instances sorted in decreasing order according to their score, then their length on the query and finally their initial order
139 #
140 # @param lAligns: list of Align instances
141 #
142 def getAlignListSortedByDecreasingScoreThenLength( lAligns ):
143 return sorted( lAligns, key=lambda iAlign: ( 1 / float(iAlign.getScore()), 1 / float(iAlign.getLengthOnQuery()) ) )
144
145 getAlignListSortedByDecreasingScoreThenLength = staticmethod( getAlignListSortedByDecreasingScoreThenLength )
146
147
148 ## Convert an Align file into a Path file
149 #
150 # @param alignFile string name of the input Align file
151 # @param pathFile string name of the output Path file
152 #
153 def convertAlignFileIntoPathFile( alignFile, pathFile ):
154 alignFileHandler = open( alignFile, "r" )
155 pathFileHandler = open( pathFile, "w" )
156 iAlign = Align()
157 countAlign = 0
158 while True:
159 line = alignFileHandler.readline()
160 if line == "":
161 break
162 countAlign += 1
163 iAlign.setFromString( line, "\t" )
164 pathFileHandler.write( "%i\t%s\n" % ( countAlign, iAlign.toString() ) )
165 alignFileHandler.close()
166 pathFileHandler.close()
167
168 convertAlignFileIntoPathFile = staticmethod( convertAlignFileIntoPathFile )
169
170
171 ## Sort an Align file
172 #
173 def sortAlignFile( inFile, outFile="" ):
174 if outFile == "":
175 outFile = "%s.sort" % ( inFile )
176 prg = "sort"
177 cmd = prg
178 cmd += " -k 1,1 -k 4,4 -k 2,2n -k 3,3n -k 5,5n -k 6,6n -k 8,8n"
179 cmd += " %s" % ( inFile )
180 cmd += " > %s" % ( outFile )
181 exitStatus = os.system( cmd )
182 if exitStatus != 0:
183 msg = "ERROR: '%s' returned '%i'" % ( prg, exitStatus )
184 sys.stderr.write( "%s\n" % ( msg ) )
185 sys.exit( exitStatus )
186
187 sortAlignFile = staticmethod( sortAlignFile )
188
189
190 ## Write Align instances contained in the given list
191 #
192 # @param lAlign a list of Align instances
193 # @param fileName name of the file to write the Align instances
194 # @param mode the open mode of the file ""w"" or ""a""
195 #
196 def writeListInFile( lAlign, fileName, mode="w" ):
197 fileHandler = open( fileName, mode )
198 for iAlign in lAlign:
199 iAlign.write( fileHandler )
200 fileHandler.close()
201
202 writeListInFile = staticmethod( writeListInFile )
203
204
205 ## Split a list of Align instances according to the name of the query
206 #
207 # @param lInAlign list of align instances
208 # @return lOutAlignList list of align instances lists
209 #
210 def splitAlignListByQueryName( lInAlign ):
211 lSortedAlign = sorted(lInAlign, key=lambda o: o.range_query.seqname)
212 lOutAlignList = []
213 if len(lSortedAlign) != 0 :
214 lAlignForCurrentQuery = []
215 previousQuery = lSortedAlign[0].range_query.seqname
216 for align in lSortedAlign :
217 currentQuery = align.range_query.seqname
218 if previousQuery != currentQuery :
219 lOutAlignList.append(lAlignForCurrentQuery)
220 previousQuery = currentQuery
221 lAlignForCurrentQuery = []
222 lAlignForCurrentQuery.append(align)
223
224 lOutAlignList.append(lAlignForCurrentQuery)
225
226 return lOutAlignList
227
228 splitAlignListByQueryName = staticmethod( splitAlignListByQueryName )
229
230
231 ## Create an Align file from each list of Align instances in the input list
232 #
233 # @param lAlignList list of lists with Align instances
234 # @param pattern string
235 # @param dirName string
236 #
237 def createAlignFiles( lAlignList, pattern, dirName="" ):
238 savedDir = os.getcwd()
239 nbFiles = len(lAlignList)
240 countFile = 1
241 if dirName != "" :
242 try:
243 os.makedirs(dirName)
244 except:
245 pass
246 os.chdir(dirName)
247
248 for lAlign in lAlignList:
249 fileName = "%s_%s.align" % (pattern, str(countFile).zfill(len(str(nbFiles))))
250 AlignUtils.writeListInFile(lAlign, fileName)
251 countFile += 1
252 os.chdir(savedDir)
253
254 createAlignFiles = staticmethod( createAlignFiles )
255
256
257 ## Return a list with Align instances sorted by query name, subject name, query start, query end and score
258 #
259 def sortList( lAligns ):
260 return sorted( lAligns, key=lambda iAlign: ( iAlign.getQueryName(),
261 iAlign.getSubjectName(),
262 iAlign.getQueryStart(),
263 iAlign.getQueryEnd(),
264 iAlign.getScore() ) )
265
266 sortList = staticmethod( sortList )
267
268
269 ## Return a list after merging all overlapping Align instances
270 #
271 def mergeList( lAligns ):
272 lMerged = []
273
274 lSorted = AlignUtils.sortList( lAligns )
275
276 prev_count = 0
277 for iAlign in lSorted:
278 if prev_count != len(lSorted):
279 for i in lSorted[ prev_count + 1: ]:
280 if iAlign.isOverlapping( i ):
281 iAlign.merge( i )
282 IsAlreadyInList = False
283 for newAlign in lMerged:
284 if newAlign.isOverlapping( iAlign ):
285 IsAlreadyInList = True
286 newAlign.merge( iAlign )
287 lMerged [ lMerged.index( newAlign ) ] = newAlign
288 if not IsAlreadyInList:
289 lMerged.append( iAlign )
290 prev_count += 1
291
292 return lMerged
293
294 mergeList = staticmethod( mergeList )
295
296
297 ## Merge all Align instance in a given Align file
298 #
299 def mergeFile( inFile, outFile="" ):
300 if outFile == "":
301 outFile = "%s.merged" % ( inFile )
302 if os.path.exists( outFile ):
303 os.remove( outFile )
304
305 tmpFile = "%s.sorted" % ( inFile )
306 AlignUtils.sortAlignFile( inFile, tmpFile )
307
308 tmpF = open( tmpFile, "r" )
309 dQrySbj2Aligns = {}
310 prevPairQrySbj = ""
311 while True:
312 line = tmpF.readline()
313 if line == "":
314 break
315 iAlign = Align()
316 iAlign.setFromString( line )
317 pairQrySbj = "%s_%s" % ( iAlign.getQueryName(), iAlign.getSubjectName() )
318 if not dQrySbj2Aligns.has_key( pairQrySbj ):
319 if prevPairQrySbj != "":
320 lMerged = AlignUtils.mergeList( dQrySbj2Aligns[ prevPairQrySbj ] )
321 AlignUtils.writeListInFile( lMerged, outFile, "a" )
322 del dQrySbj2Aligns[ prevPairQrySbj ]
323 prevPairQrySbj = pairQrySbj
324 else:
325 prevPairQrySbj = pairQrySbj
326 dQrySbj2Aligns[ pairQrySbj ] = []
327 dQrySbj2Aligns[ pairQrySbj ].append( iAlign )
328 lMerged = []
329 if len(dQrySbj2Aligns.keys()) > 0:
330 lMerged = AlignUtils.mergeList( dQrySbj2Aligns[ prevPairQrySbj ] )
331 AlignUtils.writeListInFile( lMerged, outFile, "a" )
332 tmpF.close()
333 os.remove( tmpFile )
334
335 mergeFile = staticmethod( mergeFile )
336
337
338 ## Update the scores of each match in the input file
339 #
340 # @note the new score is the length on the query times the percentage of identity
341 #
342 def updateScoresInFile( inFile, outFile ):
343 inHandler = open( inFile, "r" )
344 outHandler = open( outFile, "w" )
345 iAlign = Align()
346
347 while True:
348 line = inHandler.readline()
349 if line == "":
350 break
351 iAlign.reset()
352 iAlign.setFromString( line, "\t" )
353 iAlign.updateScore()
354 iAlign.write( outHandler )
355
356 inHandler.close()
357 outHandler.close()
358
359 updateScoresInFile = staticmethod( updateScoresInFile )