annotate commons/core/parsing/PklParser.py @ 14:c79b9ae3f65f

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author m-zytnicki
date Fri, 19 Apr 2013 10:13:11 -0400
parents 769e306b7933
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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 import re
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31 import sys
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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.Interval import Interval
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37 from commons.core.parsing.TranscriptListParser import TranscriptListParser
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38 from SMART.Java.Python.structure.Transcript import Transcript
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39
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40
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41 class PklParser(TranscriptListParser):
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42 """A class that parses the intern PKL file and create a transcript list"""
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43
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44 def __init__(self, fileName, verbosity = 1):
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45 self.title = None
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46 super(PklParser, self).__init__(fileName, verbosity)
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47 self.handle = open(fileName, "rb")
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48 self.verbosity = verbosity
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49 self.initAddress = 0
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50 self.address = self.initAddress
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51 self.over = False
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52 self.chromosome = None
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53
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54 def __del__(self):
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55 super(PklParser, self).__del__()
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56
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57 def getFileFormats():
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58 return ["pkl"]
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59 getFileFormats = staticmethod(getFileFormats)
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60
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61
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62 def skipFirstLines(self):
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63 return
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65
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66 def reset(self):
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67 self.handle.seek(0)
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68 self.initAddress = 0
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71 def setChromosome(self, chromosome):
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72 self.chromosome = chromosome
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73
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75 def gotoAddress(self, address):
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76 self.handle.seek(address)
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77 self.address = address
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78
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79
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80 def getNextTranscript(self):
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81 self.address = self.handle.tell()
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82 try:
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83 transcript = pickle.load(self.handle)
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84 if self.chromosome != None and transcript.getChromosome() != self.chromosome:
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85 self.over = True
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86 return False
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87 return transcript
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88 except EOFError:
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89 self.over = True
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90 return False
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91
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93 def getIterator(self):
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94 self.gotoAddress(self.initAddress)
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95 while True:
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96 transcript = self.getNextTranscript()
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97 if not transcript:
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98 self.over = True
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99 return
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100 yield transcript
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101
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102
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103 def setInitAddress(self, address):
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104 self.initAddress = address
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105
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106
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107 def getCurrentTranscriptAddress(self):
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108 return self.address
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109
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110
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111 def isOver(self):
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112 return self.over