Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/PklParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
---|---|
date | Thu, 17 Jan 2013 10:52:14 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:e0f8dcca02ed |
---|---|
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 try: | |
33 import cPickle as pickle | |
34 except: | |
35 import pickle | |
36 from SMART.Java.Python.structure.Interval import Interval | |
37 from commons.core.parsing.TranscriptListParser import TranscriptListParser | |
38 from SMART.Java.Python.structure.Transcript import Transcript | |
39 | |
40 | |
41 class PklParser(TranscriptListParser): | |
42 """A class that parses the intern PKL file and create a transcript list""" | |
43 | |
44 def __init__(self, fileName, verbosity = 1): | |
45 self.title = None | |
46 super(PklParser, self).__init__(fileName, verbosity) | |
47 self.handle = open(fileName, "rb") | |
48 self.verbosity = verbosity | |
49 self.initAddress = 0 | |
50 self.address = self.initAddress | |
51 self.over = False | |
52 self.chromosome = None | |
53 | |
54 def __del__(self): | |
55 super(PklParser, self).__del__() | |
56 | |
57 def getFileFormats(): | |
58 return ["pkl"] | |
59 getFileFormats = staticmethod(getFileFormats) | |
60 | |
61 | |
62 def skipFirstLines(self): | |
63 return | |
64 | |
65 | |
66 def reset(self): | |
67 self.handle.seek(0) | |
68 self.initAddress = 0 | |
69 | |
70 | |
71 def setChromosome(self, chromosome): | |
72 self.chromosome = chromosome | |
73 | |
74 | |
75 def gotoAddress(self, address): | |
76 self.handle.seek(address) | |
77 self.address = address | |
78 | |
79 | |
80 def getNextTranscript(self): | |
81 self.address = self.handle.tell() | |
82 try: | |
83 transcript = pickle.load(self.handle) | |
84 if self.chromosome != None and transcript.getChromosome() != self.chromosome: | |
85 self.over = True | |
86 return False | |
87 return transcript | |
88 except EOFError: | |
89 self.over = True | |
90 return False | |
91 | |
92 | |
93 def getIterator(self): | |
94 self.gotoAddress(self.initAddress) | |
95 while True: | |
96 transcript = self.getNextTranscript() | |
97 if not transcript: | |
98 self.over = True | |
99 return | |
100 yield transcript | |
101 | |
102 | |
103 def setInitAddress(self, address): | |
104 self.initAddress = address | |
105 | |
106 | |
107 def getCurrentTranscriptAddress(self): | |
108 return self.address | |
109 | |
110 | |
111 def isOver(self): | |
112 return self.over |