Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/TranscriptListParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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 sys | |
31 from SMART.Java.Python.structure.TranscriptList import TranscriptList | |
32 from SMART.Java.Python.misc.Progress import Progress | |
33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress | |
34 | |
35 class TranscriptListParser(object): | |
36 """A (quite generic) class that reads a list of transcripts""" | |
37 | |
38 def __init__(self, fileName, verbosity = 0): | |
39 self.verbosity = verbosity | |
40 self.fileName = fileName | |
41 self.nbTranscripts = None | |
42 self.size = None | |
43 self.chromosomes = None | |
44 self.currentTranscript = None | |
45 self.currentLineNb = 0 | |
46 self.previousTranscriptAddress = None | |
47 try: | |
48 self.handle = open(self.fileName) | |
49 except IOError: | |
50 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName)) | |
51 self.skipFirstLines() | |
52 | |
53 | |
54 def __del__(self): | |
55 self.close() | |
56 | |
57 | |
58 def getFileFormats(): | |
59 pass | |
60 getFileFormats = staticmethod(getFileFormats) | |
61 | |
62 | |
63 def close(self): | |
64 if self.handle != None and not self.handle.close: | |
65 self.handle.close() | |
66 self.handle = None | |
67 | |
68 | |
69 def reset(self): | |
70 self.handle.seek(0) | |
71 self.skipFirstLines() | |
72 self.currentTranscript = None | |
73 self.currentLineNb = 0 | |
74 self.currentTranscriptAddress = self.handle.tell() | |
75 self.currentAddress = self.handle.tell() | |
76 | |
77 | |
78 def gotoAddress(self, address): | |
79 self.reset() | |
80 self.handle.seek(address) | |
81 self.currentTranscriptAddress = address | |
82 self.currentAddress = address | |
83 | |
84 | |
85 def parse(self): | |
86 transcriptList = TranscriptList() | |
87 progress = Progress(self.getNbTranscripts(), "Reading %s" % (self.fileName), self.verbosity) | |
88 for line in self.handle: | |
89 self.currentLineNb += 1 | |
90 transcript = self.parseLine(line) | |
91 transcriptList.addTranscript(transcript) | |
92 progress.inc() | |
93 progress.done() | |
94 return transcriptList | |
95 | |
96 | |
97 def getIterator(self): | |
98 self.reset() | |
99 transcript = self.getNextTranscript() | |
100 while transcript != None: | |
101 yield transcript | |
102 transcript = self.getNextTranscript() | |
103 | |
104 | |
105 def getCurrentAddress(self): | |
106 return self.currentAddress | |
107 | |
108 | |
109 def getCurrentTranscriptAddress(self): | |
110 return self.currentTranscriptAddress | |
111 | |
112 | |
113 def getNextTranscript(self): | |
114 self.currentAddress = self.handle.tell() | |
115 line = self.handle.readline() | |
116 while line != "": | |
117 line = line.strip() | |
118 self.currentLineNb += 1 | |
119 transcript = self.parseLine(line) | |
120 if transcript != None: | |
121 return transcript | |
122 self.currentAddress = self.handle.tell() | |
123 line = self.handle.readline() | |
124 transcript = self.currentTranscript | |
125 self.currentTranscriptAddress = self.previousTranscriptAddress | |
126 self.currentTranscript = None | |
127 return transcript | |
128 | |
129 | |
130 def getInfos(self): | |
131 self.chromosomes = set() | |
132 self.nbTranscripts = 0 | |
133 self.size = 0 | |
134 self.reset() | |
135 progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9) | |
136 transcript = self.getNextTranscript() | |
137 for transcript in self.getIterator(): | |
138 self.chromosomes.add(transcript.getChromosome()) | |
139 self.nbTranscripts += 1 | |
140 self.size += transcript.getSize() | |
141 progress.inc() | |
142 progress.done() | |
143 self.reset() | |
144 | |
145 | |
146 def getNbTranscripts(self): | |
147 if self.nbTranscripts != None: | |
148 return self.nbTranscripts | |
149 self.getInfos() | |
150 return self.nbTranscripts | |
151 | |
152 | |
153 def getNbItems(self): | |
154 return self.getNbTranscripts() | |
155 | |
156 | |
157 def getChromosomes(self): | |
158 if self.chromosomes != None: | |
159 return self.chromosomes | |
160 self.getInfos() | |
161 return self.chromosomes | |
162 | |
163 | |
164 def getSize(self): | |
165 if self.size != None: | |
166 return self.size | |
167 self.getInfos() | |
168 return self.size | |
169 | |
170 | |
171 def getNbNucleotides(self): | |
172 return self.getSize() | |
173 | |
174 | |
175 def setDefaultTagValue(self, name, value): | |
176 for transcript in self.getIterator(): | |
177 transcript.setTag(name, value) | |
178 | |
179 def __eq__(self, o): | |
180 if o == None: | |
181 return False | |
182 return self.fileName == o.fileName and self.nbTranscripts == o.nbTranscripts and self.size == o.size and self.chromosomes == o.chromosomes |