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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() |
