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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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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 import optparse
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32 import os
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33 from commons.core.parsing.BlatParser import BlatParser
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34
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35 class BlatToGff(object):
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36
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37
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38 def __init__(self):
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39 pass
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40
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41 def setAttributesFromCmdLine(self):
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42 help = '\
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43 \nThis Script Launch BlatToGff.\n\n\
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44 Example 1: python BlatToGff.py -i blatResultsFile.tab -o outputFile.gff3\n\n'
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45 parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
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46 parser.add_option( '-i', '--input', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None )
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47 parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
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48 parser.add_option( '-n', '--methodname', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
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49 ( options, args ) = parser.parse_args()
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50 self._options = options
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51
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52 def checkOptions(self):
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53 if self._options.inputBLAT == '':
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54 raise Exception("ERROR: No Blat file specified for -i !")
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55 elif not os.path.exists(self._options.inputBLAT):
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56 raise Exception("ERROR: Blat Input File doesn't exist !")
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57 else:
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58 self._inputFileBlat = self._options.inputBLAT
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59
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60 if self._options.output == '':
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61 raise Exception("ERROR: No Output file specified for -o !")
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62 else:
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63 self._outputFileGFF = self._options.output
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64
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65 self._methodName = self._options.methodName
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66
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67 def run(self):
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68 self.checkOptions()
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69 self._createGFFOutputFile()
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70 BLATFile = open(self._inputFileBlat, 'r')
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71
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72 headerBlatLine = BLATFile.readline()
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73 headerBlatLine = BLATFile.readline()
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74 headerBlatLine = BLATFile.readline()
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75 headerBlatLine = BLATFile.readline()
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76 headerBlatLine = BLATFile.readline()
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77 blatLine = BLATFile.readline()
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78 numberLine = 6
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79 while blatLine != '':
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80 gffLine = self.convertBlatObjectToGffLine(blatLine, numberLine)
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81 self._printGFFLinesToOutputFile(gffLine)
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82 blatLine = BLATFile.readline()
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83 numberLine = numberLine + 1
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84
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85 def convertBlatObjectToGffLine(self, blatLine, numberLine):
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86 iBlatHit = BlatParser()
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87 iBlatHit.setAttributesFromString(blatLine, numberLine)
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88 col1 = iBlatHit.getTName()
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89 col2 = 'BlatToGff'
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90 if self._methodName == '' or self._methodName == None:
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91 col3 = 'BES'
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92 else:
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93 col3 = '%s:BES' % self._methodName
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94 col4 = iBlatHit.getTStart()
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95 col5 = iBlatHit.getTEnd()
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96 col6 = '.'
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97 col7 = '+'
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98 col8 = '.'
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99 col9 = 'ID=%s;Name=%s;bes_start=%s;bes_end=%s;bes_size=%s' % (iBlatHit.getQName(), iBlatHit.getQName(), iBlatHit.getTStart(), iBlatHit.getTEnd(), iBlatHit.getTSize())
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100 gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
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101 return gffLine
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102
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103 def _createGFFOutputFile(self):
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104 GFFfile = open(self._outputFileGFF, 'w')
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105 GFFfile.write("##gff-version 3\n")
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106 GFFfile.close()
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107
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108 def _printGFFLinesToOutputFile(self, line):
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109 GFFfile = open(self._outputFileGFF, 'a')
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110 GFFfile.write(line)
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111 GFFfile.close()
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112
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113 if __name__ == '__main__':
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114 iBlatToGff = BlatToGff()
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115 iBlatToGff.setAttributesFromCmdLine()
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116 iBlatToGff.run() |
