Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/WigParser.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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children | 94ab73e8a190 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 # | |
2 # Copyright INRA-URGI 2009-2010 | |
3 # | |
4 # This software is governed by the CeCILL license under French law and | |
5 # abiding by the rules of distribution of free software. You can use, | |
6 # modify and/ or redistribute the software under the terms of the CeCILL | |
7 # license as circulated by CEA, CNRS and INRIA at the following URL | |
8 # "http://www.cecill.info". | |
9 # | |
10 # As a counterpart to the access to the source code and rights to copy, | |
11 # modify and redistribute granted by the license, users are provided only | |
12 # with a limited warranty and the software's author, the holder of the | |
13 # economic rights, and the successive licensors have only limited | |
14 # liability. | |
15 # | |
16 # In this respect, the user's attention is drawn to the risks associated | |
17 # with loading, using, modifying and/or developing or reproducing the | |
18 # software by the user in light of its specific status of free software, | |
19 # that may mean that it is complicated to manipulate, and that also | |
20 # therefore means that it is reserved for developers and experienced | |
21 # professionals having in-depth computer knowledge. Users are therefore | |
22 # encouraged to load and test the software's suitability as regards their | |
23 # requirements in conditions enabling the security of their systems and/or | |
24 # data to be ensured and, more generally, to use and operate it in the | |
25 # same conditions as regards security. | |
26 # | |
27 # The fact that you are presently reading this means that you have had | |
28 # knowledge of the CeCILL license and that you accept its terms. | |
29 # | |
30 import re | |
31 import sys | |
32 import os.path | |
33 import struct | |
34 from commons.core.parsing.TranscriptListParser import TranscriptListParser | |
35 from SMART.Java.Python.structure.Transcript import Transcript | |
36 | |
37 STRANDTOSTR = {1: "(+)", 0: "(=)", None: "(=)", -1: "(-)"} | |
38 | |
39 nbOpenHandles = 30 | |
40 | |
41 | |
42 class WigParser(TranscriptListParser): | |
43 """A class that parses a big WIG file, creates an index and make it possible to quickly retrieve some data""" | |
44 | |
45 def __init__(self, fileName, verbosity = 1): | |
46 self.fileName = fileName | |
47 self.filler = "\xFF" * struct.calcsize('Q') | |
48 self.strands = False | |
49 self.indexFiles = {} | |
50 self.indexBuilt = False | |
51 self.defaultValue = 0.0 | |
52 self.currentChromosome = None | |
53 self.currentStrand = 1 | |
54 self.verbosity = verbosity | |
55 super(WigParser, self).__init__(fileName, verbosity) | |
56 | |
57 | |
58 def __def__(self): | |
59 for file in self.indexFiles.values(): | |
60 file.close() | |
61 | |
62 | |
63 def setStrands(self, strands): | |
64 self.strands = strands | |
65 | |
66 | |
67 def setDefaultValue(self, value): | |
68 self.defaultValue = value | |
69 | |
70 | |
71 def getFileFormats(): | |
72 return ["wig"] | |
73 getFileFormats = staticmethod(getFileFormats) | |
74 | |
75 | |
76 def setStrands(self, strands): | |
77 """ | |
78 Consider both strands separately | |
79 """ | |
80 self.strands = strands | |
81 | |
82 | |
83 def makeIndexName(self, chromosome, strand = None): | |
84 """ | |
85 Create an index name for a file | |
86 """ | |
87 directoryName = os.path.dirname(self.fileName) | |
88 if strand == None: | |
89 strandName = "" | |
90 else: | |
91 strandName = "+" if strand == 1 else "-" | |
92 indexName = os.path.join(directoryName, ".%s%s.index" % (chromosome, strandName)) | |
93 return indexName | |
94 | |
95 | |
96 def findIndexFile(self, chromosome, strand = None): | |
97 """ | |
98 Check if the index of a file exists | |
99 """ | |
100 indexName = self.makeIndexName(chromosome, strand) | |
101 if os.path.exists(indexName): | |
102 return indexName | |
103 return False | |
104 | |
105 | |
106 def makeIndexFile(self): | |
107 """ | |
108 Create the index for a file | |
109 """ | |
110 if self.indexBuilt: | |
111 return | |
112 | |
113 inputFile = open(self.fileName) | |
114 outputFile = None | |
115 index = 0 | |
116 mark = inputFile.tell() | |
117 line = inputFile.readline().strip() | |
118 chromosome = None | |
119 | |
120 while line != "": | |
121 m1 = re.search(r"^\s*-?\d+\.?\d*\s*$", line) | |
122 m2 = re.search(r"^\s*(\d+)\s+-?\d+\.?\d*\s*$", line) | |
123 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=1\s*$", line) | |
124 m4 = re.search(r"^\s*fixedStep\s+chrom=\S+\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line) | |
125 m5 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line) | |
126 m6 = re.search(r"^\s*variableStep\s+chrom=(\S+)span=(\d+)\s*$", line) | |
127 | |
128 if m1 != None: | |
129 outputFile.write(struct.pack("Q", mark)) | |
130 index += 1 | |
131 elif m2 != None: | |
132 nextIndex = int(m2.group(1)) | |
133 if index < nextIndex - 1: | |
134 outputFile.write(self.filler * (nextIndex - index - 1)) | |
135 outputFile.write(struct.pack("Q", mark)) | |
136 index = nextIndex | |
137 elif m3 != None: | |
138 newChromosome = m3.group(1) | |
139 if newChromosome != chromosome: | |
140 if outputFile != None: | |
141 outputFile.close() | |
142 outputFile = open(self.makeIndexName(newChromosome), "wb") | |
143 chromosome = newChromosome | |
144 nextIndex = int(m3.group(2)) | |
145 outputFile.write(self.filler * (nextIndex - index)) | |
146 index = nextIndex | |
147 elif m4 != None: | |
148 raise Exception("Error! Cannot parse fixed step WIG files with step > 1 or span > 1") | |
149 elif m5 != None: | |
150 newChromosome = m5.group(1) | |
151 if newChromosome != chromosome: | |
152 if outputFile != None: | |
153 outputFile.close() | |
154 outputFile = open(self.makeIndexName(newChromosome), "wb") | |
155 index = 0 | |
156 outputFile.write(self.filler) | |
157 chromosome = newChromosome | |
158 elif m6 != None: | |
159 raise Exception("Error! Cannot parse variable step WIG files with step > 1 or span > 1") | |
160 elif (len(line) == 0) or line[0] == "#" or line.startswith("track"): | |
161 pass | |
162 else: | |
163 raise Exception("Error! Cannot understand line '%s' of WIG file while creating index file! Aborting." % (line)) | |
164 | |
165 mark = inputFile.tell() | |
166 line = inputFile.readline().strip() | |
167 | |
168 inputFile.close | |
169 if outputFile != None: | |
170 outputFile.close() | |
171 self.indexBuilt = True | |
172 | |
173 | |
174 def getIndexFileHandle(self, chromosome, strand = None): | |
175 """ | |
176 Get the handle of an index file | |
177 """ | |
178 indexFileKey = chromosome | |
179 if strand != None: | |
180 indexFileKey += "+" if strand == 1 else "-" | |
181 if indexFileKey in self.indexFiles: | |
182 return self.indexFiles[indexFileKey] | |
183 | |
184 indexFileName = self.makeIndexName(chromosome, strand) | |
185 if not self.findIndexFile(chromosome, strand): | |
186 self.makeIndexFile() | |
187 | |
188 if not os.path.exists(indexFileName): | |
189 print "Warning! Index for chromosome %s, strand %s does not exist." % (chromosome, STRANDTOSTR[strand]) | |
190 return False | |
191 indexFile = open(indexFileName, "rb") | |
192 | |
193 if len(self.indexFiles.keys()) > nbOpenHandles: | |
194 removedKey = set(self.indexFiles.keys()).pop() | |
195 self.indexFiles[removedKey].close() | |
196 del self.indexFiles[removedKey] | |
197 self.indexFiles[indexFileKey] = indexFile | |
198 return indexFile | |
199 | |
200 | |
201 | |
202 def findIndex(self, chromosome, start, strand = None): | |
203 """ | |
204 Find the point where to start reading file | |
205 """ | |
206 | |
207 sizeOfLong = struct.calcsize("Q") | |
208 empty = int(struct.unpack("Q", self.filler)[0]) | |
209 offset = empty | |
210 indexFile = self.getIndexFileHandle(chromosome, strand) | |
211 | |
212 if not indexFile: | |
213 return (None, None) | |
214 | |
215 while offset == empty: | |
216 address = start * sizeOfLong | |
217 indexFile.seek(address, os.SEEK_SET) | |
218 | |
219 buffer = indexFile.read(sizeOfLong) | |
220 if len(buffer) != sizeOfLong: | |
221 if buffer == "": | |
222 print "Warning! Index position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand]) | |
223 return (None, None) | |
224 else: | |
225 raise Exception("Problem fetching position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand])) | |
226 | |
227 offset = int(struct.unpack("Q", buffer)[0]) | |
228 start += 1 | |
229 | |
230 start -= 1 | |
231 return (offset, start) | |
232 | |
233 | |
234 | |
235 def getRange(self, chromosome, start, end): | |
236 """ | |
237 Parse a wig file and output a range | |
238 """ | |
239 arrays = {} | |
240 strands = {1: "+", -1: "-"} if self.strands else {0: ""} | |
241 | |
242 for strand in strands: | |
243 | |
244 array = [self.defaultValue] * (end - start + 1) | |
245 file = open(self.fileName) | |
246 offset, index = self.findIndex(chromosome, start, strand if self.strands else None) | |
247 if offset == None: | |
248 arrays[strand] = array | |
249 continue | |
250 file.seek(offset, os.SEEK_SET) | |
251 | |
252 for line in file: | |
253 line = line.strip() | |
254 | |
255 m1 = re.search(r"^\s*(-?\d+\.?\d*)\s*$", line) | |
256 m2 = re.search(r"^\s*(\d+)\s+(-?\d+\.?\d*)\s*$", line) | |
257 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=\d+\s*$", line) | |
258 m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line) | |
259 | |
260 if m1 != None: | |
261 if index > end: | |
262 break | |
263 if index >= start: | |
264 array[index - start] = float(m1.group(1)) | |
265 index += 1 | |
266 elif m2 != None: | |
267 index = int(m2.group(1)) | |
268 if index > end: | |
269 break | |
270 if index >= start: | |
271 array[index - start] = float(m2.group(2)) | |
272 index += 1 | |
273 elif m3 != None: | |
274 if m3.group(1) != "%s%s" % (chromosome, strands[strand]): | |
275 break | |
276 index = int(m3.group(2)) | |
277 elif m4 != None: | |
278 if m4.group(1) != "%s%s" % (chromosome, strands[strand]): | |
279 break | |
280 elif (len(line) == 0) or (line[0] == "#") or line.startswith("track"): | |
281 pass | |
282 else: | |
283 raise Exception("Error! Cannot read line '%s' of wig file" % (line)) | |
284 | |
285 file.close() | |
286 | |
287 arrays[strand] = array | |
288 | |
289 if self.strands: | |
290 return arrays | |
291 return array | |
292 | |
293 | |
294 def skipFirstLines(self): | |
295 return | |
296 | |
297 | |
298 def parseLine(self, line): | |
299 if line.startswith("track"): | |
300 return None | |
301 m = re.search(r"^\s*variableStep\s+chrom=(\S+)", line) | |
302 if m != None: | |
303 chromosome = m.group(1) | |
304 if chromosome.endswith("+"): | |
305 self.currentStrand = 1 | |
306 self.currentChromosome = chromosome[:-1] | |
307 elif chromosome.endswith("-"): | |
308 self.currentStrand = -1 | |
309 self.currentChromosome = chromosome[:-1] | |
310 else: | |
311 self.currentStrand = 1 | |
312 self.currentChromosome = chromosome | |
313 return None | |
314 position, value = line.split() | |
315 position = int(position) | |
316 value = float(value) | |
317 transcript = Transcript() | |
318 transcript.setChromosome(self.currentChromosome) | |
319 transcript.setStart(position) | |
320 transcript.setEnd(position) | |
321 transcript.setDirection(self.currentStrand) | |
322 transcript.setTagValue("ID", "wig_%s_%d_%d" % (self.currentChromosome, self.currentStrand, position)) | |
323 transcript.setTagValue("nbElements", value) | |
324 return transcript |