Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/NCListParser.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
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2012
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3 #
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4 # 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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5 # 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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6 # 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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7 # 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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8 # "http://www.cecill.info".
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # 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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11 # 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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12 # 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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13 # 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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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
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16 # 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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17 # 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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18 # 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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19 # 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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20 # 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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21 # 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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22 # 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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23 # 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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24 # 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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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # 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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29 #
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30 import re
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31 import sys
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32 from commons.core.parsing.TranscriptListParser import TranscriptListParser
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33 from SMART.Java.Python.structure.Transcript import Transcript
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34 from SMART.Java.Python.structure.Interval import Interval
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35 from SMART.Java.Python.ncList.NCList import NCList
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36 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
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37 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
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38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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39 try:
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40 import cPickle as pickle
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41 except:
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42 import pickle
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43
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44
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45 class NCListParser(TranscriptListParser):
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46
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47
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48 def __init__(self, fileName, verbosity = 0):
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49 self.title = None
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50 TranscriptListParser.__init__(self, fileName, verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 self.parse()
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52
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53 def getFileFormats():
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54 return ["nclist"]
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55 getFileFormats = staticmethod(getFileFormats)
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56
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57 def skipFirstLines(self):
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58 return
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59
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60 def parse(self):
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61 handle = open(self.fileName)
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62 self.sortedFileNames = pickle.load(handle)
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63 self.nbElements = pickle.load(handle)
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64 self.nbElementsPerChromosome = pickle.load(handle)
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65 self.ncLists = pickle.load(handle)
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66 for ncList in self.ncLists.values():
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67 ncList._reopenFiles()
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68 handle.close()
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69 self.chromosomes = sorted(self.nbElementsPerChromosome.keys())
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70 self.fileNames = dict([chromosome, self.ncLists[chromosome]._transcriptFileName] for chromosome in self.chromosomes)
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71 self.currentReader = None
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72 self.currentChrIndex = 0
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73
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74 def getSortedFileNames(self):
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75 return self._sortedFileNames
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76
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77 def getNbElements(self):
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78 return self._nbElements
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79
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80 def getNbElementsPerChromosome(self):
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81 return self._nbElementsPerChromosome
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82
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83 def getNCLists(self):
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84 return self._ncLists
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85
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86 def reset(self):
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87 self.currentChrIndex = 0
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88 self.currentReader = None
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89
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90 def gotoAddress(self, address):
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91 self.currentReader.gotoAddress(address)
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92
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93 def getCurrentAddress(self):
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94 return self.getCurrentTranscriptAddress()
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95
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96 def getCurrentTranscriptAddress(self):
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97 if self.currentReader == None:
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98 return 0
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99 return self.currentReader.getCurrentTranscriptAddress()
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100
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101 def getNextTranscript(self):
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102 if self.currentReader == None:
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103 self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[0]])
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104 transcript = self.currentReader.getNextTranscript()
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105 if transcript == False:
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106 self.currentChrIndex += 1
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107 if self.currentChrIndex >= len(self.chromosomes):
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108 return None
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109 self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[self.currentChrIndex]])
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110 transcript = self.currentReader.getNextTranscript()
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111 return transcript
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112
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113 def getInfos(self):
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114 self.size = 0
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115 self.reset()
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116 progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9)
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117 transcript = self.getNextTranscript()
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118 for transcript in self.getIterator():
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119 self.size += transcript.getSize()
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120 progress.inc()
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121 progress.done()
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122 self.reset()
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123
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124 def getNbTranscripts(self):
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125 return self.nbElements