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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31
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32 import struct
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33 try:
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34 import cPickle as pickle
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35 except:
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36 import pickle
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37 from SMART.Java.Python.ncList.NCList import NCList
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38 from SMART.Java.Python.ncList.NCIndex import NCIndex
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39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
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40
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41 LONG_SIZE = struct.calcsize('l')
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42
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43 INFO_PER_NCLIST = 5
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44 H_FILE = 0
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45 L_FILE = 1
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46 G_FILE = 2
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47 FIRST_LIST_SIZE = 3
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48 INDEX = 4
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49
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50 H = 0
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51 L = 1
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52 T = 2
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53 G = 3
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54
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55 def pack(input):
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56 return struct.pack("l", long(input))
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57 def unpack(input):
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58 return struct.unpack("l", input)[0]
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59
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60
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61 class NCListHandler(object):
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62
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63 def __init__(self, verbosity):
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64 self._verbosity = verbosity
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65 self._index = False
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66
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67 def setFileName(self, fileName):
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68 self._fileName = fileName
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69 self._handle = open(fileName, "rb")
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70
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71 def loadData(self):
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72 self._chromosomes = pickle.load(self._handle)
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73 self._nbElements = 0
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74 self._nbElementsPerChromosome = {}
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75 self._ncLists = {}
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76 for chromosome in self._chromosomes:
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77 self._nbElementsPerChromosome[chromosome] = unpack(self._handle.read(LONG_SIZE))
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78 self._nbElements += self._nbElementsPerChromosome[chromosome]
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79 self._headerPos = self._handle.tell()
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80 for i, chromosome in enumerate(self._chromosomes):
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81 ncList = NCList(self._verbosity)
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82 ncList._hHandle = self._handle
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83 ncList._lHandle = self._handle
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84 ncList._parser = NCListFileUnpickle(self._fileName)
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85 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + H_FILE * LONG_SIZE)
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86 ncList.setOffset(H, unpack(self._handle.read(LONG_SIZE)))
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87 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + L_FILE * LONG_SIZE)
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88 ncList.setOffset(L, unpack(self._handle.read(LONG_SIZE)))
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89 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE)
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90 ncList.setOffset(G, unpack(self._handle.read(LONG_SIZE)))
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91 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + FIRST_LIST_SIZE * LONG_SIZE)
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92 ncList._sizeFirstList = unpack(self._handle.read(LONG_SIZE))
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93 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + INDEX * LONG_SIZE)
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94 indices = unpack(self._handle.read(LONG_SIZE))
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95 if indices != -1:
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96 self._handle.seek(indices)
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97 data = pickle.load(self._handle)
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98 index = NCIndex(self._verbosity)
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99 index._indices = data
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100 ncList._index = index
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101 self._ncLists[chromosome] = ncList
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102
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103 def getChromosomes(self):
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104 return self._chromosomes
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105
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106 def getNbElements(self):
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107 return self._nbElements
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108
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109 def getNbElementsPerChromosome(self):
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110 return self._nbElementsPerChromosome
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111
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112 def getNCLists(self):
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113 return self._ncLists
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114
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115 def getParser(self, chromosome = None):
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116 parser = NCListFileUnpickle(self._fileName)
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117 if chromosome == None:
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118 parser.setInitAddress(unpack(self._handle, self._headerPos + G_FILE * LONG_SIZE))
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119 return parser
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120 i = self._chromosomes.index(chromosome)
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121 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE)
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122 pos = unpack(self._handle.read(LONG_SIZE))
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123 parser.setInitAddress(pos)
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124 parser.setChromosome(chromosome)
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125 return parser
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