Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/BlatToGff.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
115 iBlatToGff.setAttributesFromCmdLine() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
116 iBlatToGff.run() |