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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 Clean a GTF file
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33 """
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34
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35 import shlex
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36 from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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39
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40 count = {}
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41
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42 class ParsedLine(object):
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43 def __init__(self, line, cpt):
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44 self.line = line
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45 self.cpt = cpt
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46 self.parse()
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47
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48 def parse(self):
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49 self.line = self.line.strip()
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50 self.splittedLine = self.line.split(None, 8)
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51 if len(self.splittedLine) < 9:
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52 raise Exception("Line '%s' has less than 9 fields. Exiting..." % (self.line))
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53 self.type = self.splittedLine[2]
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54 self.parseOptions()
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55
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56 def parseOptions(self):
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57 self.parsedOptions = {}
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58 key = None
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59 value = ""
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60 for option in shlex.split(self.splittedLine[8]):
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61 option = option.strip()
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62 if option == "": continue
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63 if key == None:
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64 key = option
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65 else:
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66 endValue = False
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67 if option[-1] == ";":
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68 endValue = True
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69 option.rstrip(";")
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70 value = "%s \"%s\"" % (value, option)
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71 if endValue:
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72 self.parsedOptions[key] = value
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73 if key == "transcript_id":
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74 self.transcriptId = value
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75 key = None
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76 value = ""
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77
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78 def export(self):
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79 return "%s\n" % (self.line)
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80
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81
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82 class GtfCleaner(TranscriptListCleaner):
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83
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84 def __init__(self, verbosity = 1):
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85 super(GtfCleaner, self).__init__(verbosity)
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86 self.acceptedTypes = ["exon"]
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87 self.parents = {}
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88
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89 def getFileFormats():
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90 return ["gtf"]
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91 getFileFormats = staticmethod(getFileFormats)
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92
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93 def setAcceptedTypes(self, types):
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94 self.acceptedTypes = types
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95
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96 def parse(self):
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97 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
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98 for cpt, line in enumerate(self.inputHandle):
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56
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99 if not line or (not line.strip()) or line[0] == "#": continue
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6
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100 parsedLine = ParsedLine(line, cpt)
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101 if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
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102 transcriptId = parsedLine.transcriptId
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103 if transcriptId not in self.parents:
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104 self.parents[parsedLine.transcriptId] = [parsedLine]
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105 else:
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106 self.parents[parsedLine.transcriptId].append(parsedLine)
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107 progress.inc()
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108 progress.done()
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109
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110 def write(self):
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111 progress = Progress(len(self.parents.keys()), "Writing output file", self.verbosity)
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112 for parent in sorted(self.parents.keys()):
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113 for line in self.parents[parent]:
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114 self.outputHandle.write(line.export())
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115 progress.inc()
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116 progress.done()
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117
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118 def _clean(self):
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119 self.parse()
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120 self.write()
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121
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