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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, os, shutil
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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
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38 LONG_SIZE = struct.calcsize('l')
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39
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40 INFO_PER_NCLIST = 5
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41 H_FILE = 0
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42 L_FILE = 1
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43 G_FILE = 2
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44 FIRST_LIST_SIZE = 3
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45 INDEX = 4
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46
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47 def pack(input):
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48 return struct.pack("l", long(input))
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49 def unpack(input):
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50 return struct.unpack("l", input)[0]
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51
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52
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53 class NCListMerger(object):
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54
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55 def __init__(self, verbosity):
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56 self._verbosity = verbosity
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57 self._index = False
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58
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59 def setFileName(self, fileName):
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60 self._handle = open(fileName, "wb")
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61
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62 def setNCLists(self, ncLists):
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63 self._ncLists = ncLists
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64 self._chromosomes = sorted(self._ncLists.keys())
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65
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66 def addIndex(self, boolean):
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67 self._index = boolean
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68
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69 def merge(self):
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70 self._writeHeader()
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71 self._addNCLists()
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72 self._handle.close()
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73 self._removeInputFiles()
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74
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75 def _writeHeader(self):
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76 pickle.dump(self._chromosomes, self._handle, -1)
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77 for chromosome in self._chromosomes:
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78 self._handle.write(pack(self._ncLists[chromosome]._nbLines))
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79 self._headerPos = self._handle.tell()
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80 for chromosome in self._chromosomes:
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81 for i in range(INFO_PER_NCLIST):
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82 self._handle.write(pack(-1))
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83
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84 def _addInHeader(self, i, info, value = None):
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85 currentPos = self._handle.tell()
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86 if value == None:
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87 value = currentPos
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88 self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + info * LONG_SIZE)
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89 self._handle.write(pack(value))
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90 self._handle.seek(currentPos)
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91
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92 def _addNCLists(self):
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93 self._inputFileNames = []
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94 for i, chromosome in enumerate(self._chromosomes):
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95 ncList = self._ncLists[chromosome]
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96 self._addInHeader(i, H_FILE)
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97 hFile = open(ncList._hFileName)
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98 shutil.copyfileobj(hFile, self._handle)
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99 hFile.close()
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100 self._inputFileNames.append(ncList._hFileName)
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101 for i, chromosome in enumerate(self._chromosomes):
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102 ncList = self._ncLists[chromosome]
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103 self._addInHeader(i, L_FILE)
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104 lFile = open(ncList._lFileName)
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105 shutil.copyfileobj(lFile, self._handle)
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106 lFile.close()
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107 self._inputFileNames.append(ncList._lFileName)
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108 for i, chromosome in enumerate(self._chromosomes):
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109 ncList = self._ncLists[chromosome]
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110 self._addInHeader(i, FIRST_LIST_SIZE, ncList.getSizeFirstList())
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111 if self._index:
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112 for i, chromosome in enumerate(self._chromosomes):
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113 ncList = self._ncLists[chromosome]
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114 self._addInHeader(i, INDEX)
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115 pickle.dump(ncList.getIndex()._indices, self._handle, -1)
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116 for i, chromosome in enumerate(self._chromosomes):
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117 ncList = self._ncLists[chromosome]
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118 self._addInHeader(i, G_FILE)
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119 tFile = open(ncList._transcriptFileName)
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120 shutil.copyfileobj(tFile, self._handle)
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121 tFile.close()
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122 self._inputFileNames.append(ncList._transcriptFileName)
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123
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124 def _removeInputFiles(self):
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125 for fileName in self._inputFileNames:
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126 os.remove(fileName)
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