Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/NCListParser.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 2009-2012 | |
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 from commons.core.parsing.TranscriptListParser import TranscriptListParser | |
33 from SMART.Java.Python.structure.Transcript import Transcript | |
34 from SMART.Java.Python.structure.Interval import Interval | |
35 from SMART.Java.Python.ncList.NCList import NCList | |
36 from SMART.Java.Python.ncList.NCListCursor import NCListCursor | |
37 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle | |
38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress | |
39 try: | |
40 import cPickle as pickle | |
41 except: | |
42 import pickle | |
43 | |
44 | |
45 class NCListParser(TranscriptListParser): | |
46 | |
47 | |
48 def __init__(self, fileName, verbosity = 0): | |
49 self.title = None | |
50 TranscriptListParser.__init__(self, fileName, verbosity) | |
51 self.parse() | |
52 | |
53 def getFileFormats(): | |
54 return ["nclist"] | |
55 getFileFormats = staticmethod(getFileFormats) | |
56 | |
57 def skipFirstLines(self): | |
58 return | |
59 | |
60 def parse(self): | |
61 handle = open(self.fileName) | |
62 self.sortedFileNames = pickle.load(handle) | |
63 self.nbElements = pickle.load(handle) | |
64 self.nbElementsPerChromosome = pickle.load(handle) | |
65 self.ncLists = pickle.load(handle) | |
66 for ncList in self.ncLists.values(): | |
67 ncList._reopenFiles() | |
68 handle.close() | |
69 self.chromosomes = sorted(self.nbElementsPerChromosome.keys()) | |
70 self.fileNames = dict([chromosome, self.ncLists[chromosome]._transcriptFileName] for chromosome in self.chromosomes) | |
71 self.currentReader = None | |
72 self.currentChrIndex = 0 | |
73 | |
74 def getSortedFileNames(self): | |
75 return self._sortedFileNames | |
76 | |
77 def getNbElements(self): | |
78 return self._nbElements | |
79 | |
80 def getNbElementsPerChromosome(self): | |
81 return self._nbElementsPerChromosome | |
82 | |
83 def getNCLists(self): | |
84 return self._ncLists | |
85 | |
86 def reset(self): | |
87 self.currentChrIndex = 0 | |
88 self.currentReader = None | |
89 | |
90 def gotoAddress(self, address): | |
91 self.currentReader.gotoAddress(address) | |
92 | |
93 def getCurrentAddress(self): | |
94 return self.getCurrentTranscriptAddress() | |
95 | |
96 def getCurrentTranscriptAddress(self): | |
97 if self.currentReader == None: | |
98 return 0 | |
99 return self.currentReader.getCurrentTranscriptAddress() | |
100 | |
101 def getNextTranscript(self): | |
102 if self.currentReader == None: | |
103 self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[0]]) | |
104 transcript = self.currentReader.getNextTranscript() | |
105 if transcript == False: | |
106 self.currentChrIndex += 1 | |
107 if self.currentChrIndex >= len(self.chromosomes): | |
108 return None | |
109 self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[self.currentChrIndex]]) | |
110 transcript = self.currentReader.getNextTranscript() | |
111 return transcript | |
112 | |
113 def getInfos(self): | |
114 self.size = 0 | |
115 self.reset() | |
116 progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9) | |
117 transcript = self.getNextTranscript() | |
118 for transcript in self.getIterator(): | |
119 self.size += transcript.getSize() | |
120 progress.inc() | |
121 progress.done() | |
122 self.reset() | |
123 | |
124 def getNbTranscripts(self): | |
125 return self.nbElements |