Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/ncList/NCListFilePickle.py @ 0:e0f8dcca02ed

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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
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31
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32 try:
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33 import cPickle as pickle
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34 except:
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35 import pickle
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36 from SMART.Java.Python.structure.Transcript import Transcript
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37
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38
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 class NCListFilePickle(object):
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40
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41 def __init__(self, fileName, verbosity = 1):
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42 self.fileName = fileName
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43 self.handle = open(fileName, "wb")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 self.verbosity = verbosity
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45
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46 def __del__(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 if self.handle != None:
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48 self.handle.close()
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49
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50 def addTranscript(self, transcript):
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51 pickle.dump(transcript, self.handle, -1)
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52
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53 def write(self):
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54 pass
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55
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56 def close(self):
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57 self.__del__()
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58
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59
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60 class NCListFileUnpickle(object):
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61
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62 def __init__(self, fileName, verbosity = 1):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 self.handle = open(fileName, "rb")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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64 self.verbosity = verbosity
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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65 self.initAddress = 0
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66 self.address = self.initAddress
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67 self.nbTranscripts = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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68 self.fileName = fileName
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69 self.over = False
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70 self.chromosome = None
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71
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72 def __del__(self):
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73 if self.handle != None:
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74 self.handle.close()
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75
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76 def reset(self):
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77 self.handle.seek(0)
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78 self.initAddress = 0
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79
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80 def setChromosome(self, chromosome):
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81 self.chromosome = chromosome
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82
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83 def getNbTranscripts(self):
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84 if self.nbTranscripts != None:
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85 return self._nbTranscripts
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86 self.nbTranscripts = 0
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87 for transcript in self.getIterator():
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88 self_nbTranscripts += 1
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89 return self.nbTranscripts
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90
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91 def gotoAddress(self, address):
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92 self.handle.seek(address)
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93 self.address = address
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94
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95 def getNextTranscript(self):
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96 self.address = self.handle.tell()
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97 try:
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98 transcript = pickle.load(self.handle)
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99 if self.chromosome != None and transcript.getChromosome() != self.chromosome:
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100 self.over = True
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101 return False
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102 return transcript
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103 except EOFError:
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104 self.over = True
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105 return False
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106
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107 def getIterator(self):
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108 self.gotoAddress(self.initAddress)
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109 while True:
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110 transcript = self.getNextTranscript()
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111 if not transcript:
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112 self.over = True
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113 return
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114 yield transcript
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115
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116 def setInitAddress(self, address):
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117 self.initAddress = address
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118
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119 def getCurrentTranscriptAddress(self):
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120 return self.address
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121
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122 def isOver(self):
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123 return self.over