Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/ncList/NCListHandler.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 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2010 | |
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 struct | |
33 try: | |
34 import cPickle as pickle | |
35 except: | |
36 import pickle | |
37 from SMART.Java.Python.ncList.NCList import NCList | |
38 from SMART.Java.Python.ncList.NCIndex import NCIndex | |
39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle | |
40 | |
41 LONG_SIZE = struct.calcsize('l') | |
42 | |
43 INFO_PER_NCLIST = 5 | |
44 H_FILE = 0 | |
45 L_FILE = 1 | |
46 G_FILE = 2 | |
47 FIRST_LIST_SIZE = 3 | |
48 INDEX = 4 | |
49 | |
50 H = 0 | |
51 L = 1 | |
52 T = 2 | |
53 G = 3 | |
54 | |
55 def pack(input): | |
56 return struct.pack("l", long(input)) | |
57 def unpack(input): | |
58 return struct.unpack("l", input)[0] | |
59 | |
60 | |
61 class NCListHandler(object): | |
62 | |
63 def __init__(self, verbosity): | |
64 self._verbosity = verbosity | |
65 self._index = False | |
66 | |
67 def setFileName(self, fileName): | |
68 self._fileName = fileName | |
69 self._handle = open(fileName, "rb") | |
70 | |
71 def loadData(self): | |
72 self._chromosomes = pickle.load(self._handle) | |
73 self._nbElements = 0 | |
74 self._nbElementsPerChromosome = {} | |
75 self._ncLists = {} | |
76 for chromosome in self._chromosomes: | |
77 self._nbElementsPerChromosome[chromosome] = unpack(self._handle.read(LONG_SIZE)) | |
78 self._nbElements += self._nbElementsPerChromosome[chromosome] | |
79 self._headerPos = self._handle.tell() | |
80 for i, chromosome in enumerate(self._chromosomes): | |
81 ncList = NCList(self._verbosity) | |
82 ncList._hHandle = self._handle | |
83 ncList._lHandle = self._handle | |
84 ncList._parser = NCListFileUnpickle(self._fileName) | |
85 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + H_FILE * LONG_SIZE) | |
86 ncList.setOffset(H, unpack(self._handle.read(LONG_SIZE))) | |
87 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + L_FILE * LONG_SIZE) | |
88 ncList.setOffset(L, unpack(self._handle.read(LONG_SIZE))) | |
89 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE) | |
90 ncList.setOffset(G, unpack(self._handle.read(LONG_SIZE))) | |
91 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + FIRST_LIST_SIZE * LONG_SIZE) | |
92 ncList._sizeFirstList = unpack(self._handle.read(LONG_SIZE)) | |
93 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + INDEX * LONG_SIZE) | |
94 indices = unpack(self._handle.read(LONG_SIZE)) | |
95 if indices != -1: | |
96 self._handle.seek(indices) | |
97 data = pickle.load(self._handle) | |
98 index = NCIndex(self._verbosity) | |
99 index._indices = data | |
100 ncList._index = index | |
101 self._ncLists[chromosome] = ncList | |
102 | |
103 def getChromosomes(self): | |
104 return self._chromosomes | |
105 | |
106 def getNbElements(self): | |
107 return self._nbElements | |
108 | |
109 def getNbElementsPerChromosome(self): | |
110 return self._nbElementsPerChromosome | |
111 | |
112 def getNCLists(self): | |
113 return self._ncLists | |
114 | |
115 def getParser(self, chromosome = None): | |
116 parser = NCListFileUnpickle(self._fileName) | |
117 if chromosome == None: | |
118 parser.setInitAddress(unpack(self._handle, self._headerPos + G_FILE * LONG_SIZE)) | |
119 return parser | |
120 i = self._chromosomes.index(chromosome) | |
121 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE) | |
122 pos = unpack(self._handle.read(LONG_SIZE)) | |
123 parser.setInitAddress(pos) | |
124 parser.setChromosome(chromosome) | |
125 return parser |