Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ncList/FindOverlapsWithOneInterval.py @ 36:44d5973c188c
Uploaded
author | m-zytnicki |
---|---|
date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
children |
comparison
equal
deleted
inserted
replaced
35:d94018ca4ada | 36:44d5973c188c |
---|---|
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 struct | |
33 import math | |
34 import os | |
35 from optparse import OptionParser | |
36 from commons.core.writer.Gff3Writer import Gff3Writer | |
37 from SMART.Java.Python.ncList.NCList import NCList | |
38 from SMART.Java.Python.ncList.FileSorter import FileSorter | |
39 from commons.core.parsing.ParserChooser import ParserChooser | |
40 from SMART.Java.Python.ncList.NCListCursor import NCListCursor | |
41 from SMART.Java.Python.structure.Transcript import Transcript | |
42 | |
43 LONGSIZE = struct.calcsize('l') | |
44 | |
45 class FindOverlapsWithOneInterval(object): | |
46 | |
47 def __init__(self, verbosity): | |
48 self._sortedFileName = None | |
49 self._verbosity = verbosity | |
50 self._overlappingNames = [] | |
51 self._nbOverlaps = 0 | |
52 self._nbWritten = 0 | |
53 | |
54 def __del__(self): | |
55 if self._sortedFileName and os.path.exists(self._sortedFileName): | |
56 os.remove(self._sortedFileName) | |
57 | |
58 def close(self): | |
59 self._iWriter.close() | |
60 | |
61 def setOutputFileName(self, fileName): | |
62 self._iWriter = Gff3Writer(fileName) | |
63 | |
64 def setFileName(self, fileName, format): | |
65 chooser = ParserChooser(self._verbosity) | |
66 chooser.findFormat(format) | |
67 self._parser = chooser.getParser(fileName) | |
68 self._sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0]) | |
69 | |
70 def setInterval(self, chromosome, start, end): | |
71 self._chromosome = chromosome | |
72 self._start = start | |
73 self._end = end | |
74 self._transcript = Transcript() | |
75 self._transcript.setChromosome(chromosome) | |
76 self._transcript.setStart(start) | |
77 self._transcript.setEnd(end) | |
78 self._transcript.setDirection("+") | |
79 | |
80 def setTranscript(self, transcript): | |
81 if transcript.__class__.__name__ == "Mapping": | |
82 transcript = transcript.getTranscript() | |
83 self._chromosome = transcript.getChromosome() | |
84 self._start = transcript.getStart() | |
85 self._end = transcript.getEnd() | |
86 self._transcript = transcript | |
87 | |
88 def prepareIntermediateFiles(self): | |
89 fs = FileSorter(self._parser, self._verbosity-4) | |
90 fs.selectChromosome(self._chromosome) | |
91 fs.perChromosome(False) | |
92 fs.setOutputFileName(self._sortedFileName) | |
93 fs.sort() | |
94 self._nbTotalLines = fs.getNbElements() | |
95 self._nbLines = fs.getNbElementsPerChromosome()[self._chromosome] | |
96 | |
97 def createNCList(self): | |
98 if self._verbosity > 2: | |
99 print "Creating NC-list..." | |
100 ncList = NCList(self._verbosity) | |
101 ncList.createIndex(True) | |
102 ncList.setChromosome(self._chromosome) | |
103 ncList.setFileName(self._sortedFileName) | |
104 ncList.setNbElements(self._nbTotalLines) | |
105 ncList.buildLists() | |
106 self.setNCList(ncList, ncList.getIndex()) | |
107 if self._verbosity > 2: | |
108 print " ...done (%ds)" % (endTime - startTime) | |
109 | |
110 def setNCList(self, ncList, index): | |
111 self._ncList = ncList | |
112 self._indix = index | |
113 | |
114 def binarySearch(self, cursor, startL, endL): | |
115 if startL > endL: | |
116 return None | |
117 middleL = (startL + endL) / 2 | |
118 cursor.moveSibling(middleL) | |
119 overlap = self.isOverlapping(cursor) | |
120 if overlap == 0: | |
121 if middleL == startL: | |
122 return cursor | |
123 else: | |
124 return self.binarySearch(cursor, startL, middleL) | |
125 if overlap == -1: | |
126 return self.binarySearch(cursor, middleL + 1, endL) | |
127 return self.binarySearch(cursor, startL, middleL - 1) | |
128 | |
129 def compare(self, cursor = None): | |
130 self._ncList.openFiles() | |
131 if cursor == None: | |
132 dump = True | |
133 cursor = NCListCursor(None, self._ncList, 0, self._verbosity) | |
134 cursor._getSiblingData() | |
135 cursor = self.binarySearch(cursor, cursor._firstSiblingLIndex, cursor._lastSiblingLIndex) | |
136 if cursor == None: | |
137 return | |
138 while not cursor.isOut() and self.isOverlapping(cursor) == 0: | |
139 self.write(cursor) | |
140 newCursor = NCListCursor(cursor) | |
141 if newCursor.hasChildren(): | |
142 newCursor.moveDown() | |
143 self.compare(newCursor) | |
144 if cursor.isLast(): | |
145 return | |
146 cursor.moveRight() | |
147 | |
148 def isOverlapping(self, cursor): | |
149 if self._end < cursor.getStart(): | |
150 return 1 | |
151 if self._start > cursor.getEnd(): | |
152 return -1 | |
153 return 0 | |
154 | |
155 def write(self, cursor): | |
156 self._nbOverlaps += 1 | |
157 refTranscript = cursor.getTranscript() | |
158 self._overlappingNames.append(refTranscript.getName()) | |
159 | |
160 def dumpWriter(self): | |
161 if (not self._overlappingNames) or self._transcript == None: | |
162 return | |
163 self._transcript.setTagValue("nbOverlaps", len(self._overlappingNames)) | |
164 self._transcript.setTagValue("overlapsWith", "--".join(self._overlappingNames)) | |
165 self._iWriter.addTranscript(self._transcript) | |
166 self._nbWritten += 1 | |
167 self._overlappingNames = [] | |
168 | |
169 def run(self): | |
170 self.prepareIntermediateFiles() | |
171 self.createNCList() | |
172 self.compare() | |
173 self.dumpWriter() | |
174 self.close() | |
175 if self._verbosity > 0: | |
176 print "# refs: %d" % (self._nbLines) | |
177 print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps) | |
178 | |
179 | |
180 if __name__ == "__main__": | |
181 description = "FindOverlapsWithOneInterval: Finds overlaps with one query interval." | |
182 | |
183 parser = OptionParser(description = description) | |
184 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="Input file [compulsory] [format: file in transcript format given by -f]") | |
185 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="Format of previous file [compulsory] [format: transcript file format]") | |
186 parser.add_option("-s", "--start", dest="start", action="store", type="int", help="The start of the query interval [compulsory] [format: int]") | |
187 parser.add_option("-e", "--end", dest="end", action="store", type="int", help="The end of the query interval [compulsory] [format: int]") | |
188 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", type="string", help="Chromosome of the query interval [compulsory] [format: string]") | |
189 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="Output file [compulsory] [format: output file in GFF3 format]") | |
190 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]") | |
191 (options, args) = parser.parse_args() | |
192 | |
193 iFOWOI = FindOverlapsWithOneInterval(options.verbosity) | |
194 iFOWOI.setFileName(options.inputFileName, options.format) | |
195 iFOWOI.setInterval(options.chromosome, options.start, options.end) | |
196 iFOWOI.setOutputFileName(options.outputFileName) | |
197 iFOWOI.run() |