Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ncList/NCListParser.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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5:ea3082881bf8 | 6:769e306b7933 |
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1 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2012 | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 # | |
31 | |
32 import random, os, time | |
33 from optparse import OptionParser | |
34 from commons.core.parsing.ParserChooser import ParserChooser | |
35 from SMART.Java.Python.structure.Transcript import Transcript | |
36 from SMART.Java.Python.structure.Interval import Interval | |
37 from SMART.Java.Python.ncList.NCList import NCList | |
38 from SMART.Java.Python.ncList.NCListCursor import NCListCursor | |
39 try: | |
40 import cPickle as pickle | |
41 except: | |
42 import pickle | |
43 | |
44 class NCListParser(object): | |
45 | |
46 def __init__(self, fileName, verbosity = 1): | |
47 self._fileName = fileName | |
48 self._ncLists = {} | |
49 self._sortedFileNames = {} | |
50 self._nbElements = 0 | |
51 self._nbElementsPerChromosome = {} | |
52 self._verbosity = verbosity | |
53 | |
54 def parse(self): | |
55 handle = open(self._fileName) | |
56 self._sortedFileNames = pickle.load(handle) | |
57 self._nbElements = pickle.load(handle) | |
58 self._nbElementsPerChromosome = pickle.load(handle) | |
59 self._ncLists = pickle.load(handle) | |
60 for ncList in self._ncLists.values(): | |
61 ncList._reopenFiles() | |
62 handle.close() | |
63 | |
64 def getSortedFileNames(self): | |
65 return self._sortedFileNames | |
66 | |
67 def getNbElements(self): | |
68 return self._nbElements | |
69 | |
70 def getNbElementsPerChromosome(self): | |
71 return self._nbElementsPerChromosome | |
72 | |
73 def getNCLists(self): | |
74 return self._ncLists |