Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/CrossSsrAndBesMappedByBlatToGff.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 |
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32 import os |
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33 import optparse |
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34 from commons.core.parsing.SsrParser import SsrParser |
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35 from commons.core.parsing.BlatParser import BlatParser |
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36 |
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37 class CrossSsrAndBesMappedByBlatToGff(object): |
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38 |
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39 |
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40 def __init__(self): |
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41 self._inputFileSSR = '' |
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42 self._inputFileBlat = '' |
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43 self._outputFileGFF = '' |
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44 |
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45 def setAttributesFromCmdLine(self): |
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46 help = '\ |
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47 \nThis Script Launch CrossSsrAndBesMappedByBlatToGff.\n\n\ |
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48 Example 1: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3\n\ |
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49 Example 2: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3 -n muscadine:filtre1\n\n' |
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50 |
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51 parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0") |
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52 parser.add_option( '-s', '--ssr', dest='inputSSR', help='SSR Input File Name [Format: tabular]', default= None ) |
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53 parser.add_option( '-b', '--blat', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None ) |
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54 parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None ) |
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55 parser.add_option( '-n', '--methodName', dest='methodName', help='Method name in col. 3 [Default: None]', default= None ) |
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56 ( options, args ) = parser.parse_args() |
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57 self.options = options |
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58 |
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59 def checkOptions(self): |
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60 if self.options.inputSSR == '': |
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61 raise Exception("ERROR: No SSR file specified for -s !") |
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62 elif not os.path.exists(self.options.inputSSR): |
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63 raise Exception("ERROR: SSR Input File doesn't exist !") |
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64 else: |
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65 self._inputFileSSR = self.options.inputSSR |
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66 |
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67 if self.options.inputBLAT == '': |
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68 raise Exception("ERROR: No Blat file specified for -b !") |
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69 elif not os.path.exists(self.options.inputBLAT): |
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70 raise Exception("ERROR: Blat Input File doesn't exist !") |
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71 else: |
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72 self._inputFileBlat = self.options.inputBLAT |
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73 |
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74 if self.options.output == '': |
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75 raise Exception("ERROR: No Output file specified for -o !") |
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76 else: |
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77 self._outputFileGFF = self.options.output |
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78 |
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79 self._methodName = self.options.methodName |
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80 |
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81 def run(self): |
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82 self.checkOptions() |
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83 self._createGFFOutputFile() |
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84 |
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85 dictSsrParser = {} |
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86 dictSsrParser = self.createDictOfSsrParser(dictSsrParser) |
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87 |
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88 BLATFile = open(self._inputFileBlat, 'r') |
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89 |
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90 headerBlatLine = BLATFile.readline() |
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91 headerBlatLine = BLATFile.readline() |
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92 headerBlatLine = BLATFile.readline() |
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93 headerBlatLine = BLATFile.readline() |
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94 headerBlatLine = BLATFile.readline() |
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95 blatLine = BLATFile.readline() |
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96 numberLine = 6 |
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97 while blatLine != '' and blatLine != '\n': |
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98 thisBlatHit = BlatParser() |
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99 thisBlatHit.setAttributesFromString(blatLine, numberLine) |
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100 besName = thisBlatHit.getQName() |
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101 |
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102 if besName in dictSsrParser: |
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103 lLinesToPrint = self.createListOfGFFLinesForThisBesWithSSR(thisBlatHit, dictSsrParser) |
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104 self._printGFFLinesToOutputFile(lLinesToPrint) |
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105 |
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106 blatLine = BLATFile.readline() |
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107 numberLine = numberLine + 1 |
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108 |
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109 BLATFile.close() |
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110 |
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111 def createDictOfSsrParser(self, dictSsrParser): |
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112 dictSsrParser = {} |
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113 SSRFile = open(self._inputFileSSR, 'r') |
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114 |
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115 header = SSRFile.readline() |
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116 line = SSRFile.readline() |
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117 numberLine = 2 |
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118 |
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119 while line != '' and line != '\n': |
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120 thisSSRHit = SsrParser() |
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121 thisSSRHit.setAttributesFromString(line, numberLine) |
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122 |
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123 BESName = thisSSRHit.getBesName() |
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124 if not BESName in dictSsrParser: |
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125 list = [thisSSRHit] |
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126 dictSsrParser[BESName] = list |
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127 else: |
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128 list = dictSsrParser[BESName] |
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129 list.append(thisSSRHit) |
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130 dictSsrParser[BESName] = list |
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131 |
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132 line = SSRFile.readline() |
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133 numberLine = numberLine + 1 |
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134 |
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135 SSRFile.close() |
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136 return dictSsrParser |
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137 |
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138 def createListOfGFFLinesForThisBesWithSSR(self, BlatHitObject, dictSsrParser): |
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139 listGffLines = [] |
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140 |
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141 besNameToKeep = BlatHitObject.getQName() |
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142 lOfSSRHitObject = dictSsrParser[besNameToKeep] |
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143 |
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144 for SSRHitObject in lOfSSRHitObject: |
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145 posSSRStart = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrStart(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand()) |
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146 posSSREnd = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrEnd(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand()) |
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147 ssrSeq = self.getSsrSeq(SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber()) |
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148 |
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149 col1 = BlatHitObject.getTName() |
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150 col2 = 'CrossSsrAndBesAlignedByBlat' |
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151 if self._methodName != '' and self._methodName != None: |
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152 col3 = '%s:SSR' %self._methodName |
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153 else: |
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154 col3 = 'SSR' |
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155 col4 = posSSRStart |
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156 col5 = posSSREnd |
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157 col6 = '.' |
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158 col7 = BlatHitObject.getStrand() |
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159 col8 = '.' |
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160 col9 = 'ID=SSR_%s_%s;Name=SSR_%s_%s;bes_name=%s;bes_size=%s;bes_matchstart=%s;bes_matchend=%s;bes_redundancy=%s;ssr_type=%s;ssr_motif=%s;ssr_motif_number=%s;ssr_start=%s;ssr_end=%s;muscadine_seq=%s' % (besNameToKeep, SSRHitObject.getBesRedundancy(), |
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161 besNameToKeep, SSRHitObject.getBesRedundancy(), |
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162 besNameToKeep, BlatHitObject.getQSize(), |
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163 BlatHitObject.getQStart(), BlatHitObject.getQEnd(), |
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164 SSRHitObject.getBesRedundancy(), SSRHitObject.getSsrNbNucleotides(), |
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165 SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber(), |
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166 SSRHitObject.getSsrStart(), SSRHitObject.getSsrEnd(), ssrSeq) |
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167 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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168 listGffLines.append(gffLine) |
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169 |
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170 return listGffLines |
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171 |
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172 def convertSSRPositionsToChromPositions(self, ssrPos, chromPosStart, chromPosEnd, strand): |
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173 if strand == '+': |
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174 newPos = int(chromPosStart) + int(ssrPos) - 1 |
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175 elif strand == '-': |
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176 newPos = int(chromPosEnd) - int(ssrPos) + 1 |
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177 return newPos |
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178 |
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179 def getSsrSeq(self, motif, nbMotif): |
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180 ssrSeq = motif * int(nbMotif) |
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181 return ssrSeq |
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182 |
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183 def _createGFFOutputFile(self): |
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184 GFFfile = open(self._outputFileGFF, 'w') |
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185 GFFfile.write("##gff-version 3\n") |
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186 GFFfile.close() |
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187 |
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188 def _printGFFLinesToOutputFile(self, lLinesToPrint): |
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189 GFFfile = open(self._outputFileGFF, 'a') |
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190 for line in lLinesToPrint: |
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191 GFFfile.write(line) |
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192 GFFfile.close() |
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193 |
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194 if __name__ == '__main__': |
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195 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() |
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196 iCrossSsrAndBesMappedByBlatToGff.setAttributesFromCmdLine() |
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197 iCrossSsrAndBesMappedByBlatToGff.run() |