Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/WigParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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children | 169d364ddd91 |
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35:d94018ca4ada | 36:44d5973c188c |
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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*$", line) | |
126 m6 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s+span=(\d+)\s*$", 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 if m6.group(2) != "1": | |
160 raise Exception("Error! Cannot parse variable step WIG files with step > 1 or span > 1") | |
161 newChromosome = m6.group(1) | |
162 if newChromosome != chromosome: | |
163 if outputFile != None: | |
164 outputFile.close() | |
165 outputFile = open(self.makeIndexName(newChromosome), "wb") | |
166 index = 0 | |
167 outputFile.write(self.filler) | |
168 chromosome = newChromosome | |
169 elif (len(line) == 0) or line[0] == "#" or line.startswith("track"): | |
170 pass | |
171 else: | |
172 raise Exception("Error! Cannot understand line '%s' of WIG file while creating index file! Aborting." % (line)) | |
173 | |
174 mark = inputFile.tell() | |
175 line = inputFile.readline().strip() | |
176 | |
177 inputFile.close | |
178 if outputFile != None: | |
179 outputFile.close() | |
180 self.indexBuilt = True | |
181 | |
182 | |
183 def getIndexFileHandle(self, chromosome, strand = None): | |
184 """ | |
185 Get the handle of an index file | |
186 """ | |
187 indexFileKey = chromosome | |
188 if strand != None: | |
189 indexFileKey += "+" if strand == 1 else "-" | |
190 if indexFileKey in self.indexFiles: | |
191 return self.indexFiles[indexFileKey] | |
192 | |
193 indexFileName = self.makeIndexName(chromosome, strand) | |
194 if not self.findIndexFile(chromosome, strand): | |
195 self.makeIndexFile() | |
196 | |
197 if not os.path.exists(indexFileName): | |
198 print "Warning! Index for chromosome %s, strand %s does not exist." % (chromosome, STRANDTOSTR[strand]) | |
199 return False | |
200 indexFile = open(indexFileName, "rb") | |
201 | |
202 if len(self.indexFiles.keys()) > nbOpenHandles: | |
203 removedKey = set(self.indexFiles.keys()).pop() | |
204 self.indexFiles[removedKey].close() | |
205 del self.indexFiles[removedKey] | |
206 self.indexFiles[indexFileKey] = indexFile | |
207 return indexFile | |
208 | |
209 | |
210 | |
211 def findIndex(self, chromosome, start, strand = None): | |
212 """ | |
213 Find the point where to start reading file | |
214 """ | |
215 | |
216 sizeOfLong = struct.calcsize("Q") | |
217 empty = int(struct.unpack("Q", self.filler)[0]) | |
218 offset = empty | |
219 indexFile = self.getIndexFileHandle(chromosome, strand) | |
220 | |
221 if not indexFile: | |
222 return (None, None) | |
223 | |
224 while offset == empty: | |
225 address = start * sizeOfLong | |
226 indexFile.seek(address, os.SEEK_SET) | |
227 | |
228 buffer = indexFile.read(sizeOfLong) | |
229 if len(buffer) != sizeOfLong: | |
230 if buffer == "": | |
231 print "Warning! Index position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand]) | |
232 return (None, None) | |
233 else: | |
234 raise Exception("Problem fetching position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand])) | |
235 | |
236 offset = int(struct.unpack("Q", buffer)[0]) | |
237 start += 1 | |
238 | |
239 start -= 1 | |
240 return (offset, start) | |
241 | |
242 | |
243 | |
244 def getRange(self, chromosome, start, end): | |
245 """ | |
246 Parse a wig file and output a range | |
247 """ | |
248 arrays = {} | |
249 strands = {1: "+", -1: "-"} if self.strands else {0: ""} | |
250 | |
251 for strand in strands: | |
252 | |
253 array = [self.defaultValue] * (end - start + 1) | |
254 file = open(self.fileName) | |
255 offset, index = self.findIndex(chromosome, start, strand if self.strands else None) | |
256 if offset == None: | |
257 arrays[strand] = array | |
258 continue | |
259 file.seek(offset, os.SEEK_SET) | |
260 | |
261 for line in file: | |
262 line = line.strip() | |
263 | |
264 m1 = re.search(r"^\s*(-?\d+\.?\d*)\s*$", line) | |
265 m2 = re.search(r"^\s*(\d+)\s+(-?\d+\.?\d*)\s*$", line) | |
266 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=\d+\s*$", line) | |
267 m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line) | |
268 | |
269 if m1 != None: | |
270 if index > end: | |
271 break | |
272 if index >= start: | |
273 array[index - start] = float(m1.group(1)) | |
274 index += 1 | |
275 elif m2 != None: | |
276 index = int(m2.group(1)) | |
277 if index > end: | |
278 break | |
279 if index >= start: | |
280 array[index - start] = float(m2.group(2)) | |
281 index += 1 | |
282 elif m3 != None: | |
283 if m3.group(1) != "%s%s" % (chromosome, strands[strand]): | |
284 break | |
285 index = int(m3.group(2)) | |
286 elif m4 != None: | |
287 if m4.group(1) != "%s%s" % (chromosome, strands[strand]): | |
288 break | |
289 elif (len(line) == 0) or (line[0] == "#") or line.startswith("track"): | |
290 pass | |
291 else: | |
292 raise Exception("Error! Cannot read line '%s' of wig file" % (line)) | |
293 | |
294 file.close() | |
295 | |
296 arrays[strand] = array | |
297 | |
298 if self.strands: | |
299 return arrays | |
300 return array | |
301 | |
302 | |
303 def skipFirstLines(self): | |
304 return | |
305 | |
306 | |
307 def parseLine(self, line): | |
308 if line.startswith("track"): | |
309 return None | |
310 m = re.search(r"^\s*variableStep\s+chrom=(\S+)", line) | |
311 if m != None: | |
312 chromosome = m.group(1) | |
313 if chromosome.endswith("+"): | |
314 self.currentStrand = 1 | |
315 self.currentChromosome = chromosome[:-1] | |
316 elif chromosome.endswith("-"): | |
317 self.currentStrand = -1 | |
318 self.currentChromosome = chromosome[:-1] | |
319 else: | |
320 self.currentStrand = 1 | |
321 self.currentChromosome = chromosome | |
322 return None | |
323 position, value = line.split() | |
324 position = int(position) | |
325 value = float(value) | |
326 transcript = Transcript() | |
327 transcript.setChromosome(self.currentChromosome) | |
328 transcript.setStart(position) | |
329 transcript.setEnd(position) | |
330 transcript.setDirection(self.currentStrand) | |
331 transcript.setTagValue("ID", "wig_%s_%d_%d" % (self.currentChromosome, self.currentStrand, position)) | |
332 transcript.setTagValue("nbElements", value) | |
333 return transcript |