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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 sys
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32
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33 ## this class can parse a Blat results output file
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34 #
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35 class BlatParser(object):
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36
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37
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38 def __init__(self, match='', mismatch='', repMatch='', N='', QGapCount='', QGapBases='', TGapCount='', TGapBases='', strand='', QName='', QSize='', QStart='', QEnd='', TName='', TSize='', TStart='', TEnd='', blockCount='', blockSizes='', qStarts='', tStarts=''):
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39 self._match = match
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40 self._mismatch = mismatch
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41 self._repMatch = repMatch
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42 self._N = N
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43 self._QGapCount = QGapCount
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44 self._QGapBases = QGapBases
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45 self._TGapCount = TGapCount
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46 self._TGapBases = TGapBases
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47 self._strand = strand
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48 self._QName = QName
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49 self._QSize = QSize
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50 self._QStart = QStart
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51 self._QEnd = QEnd
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52 self._TName = TName
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53 self._TSize = TSize
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54 self._TStart = TStart
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55 self._TEnd = TEnd
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56 self._blockCount = blockCount
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57 self._blockSizes = blockSizes
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58 self._qStarts = qStarts
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59 self._tStarts = tStarts
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60
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61 def __eq__(self, o):
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62 return self._TName == o._TName and self._TSize == o._TSize and self._TStart == o._TStart and self._TEnd == o._TEnd
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63
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64 def setMatch(self, match):
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65 self._match = match
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66
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67 def setMismatch(self, mismatch):
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68 self._mismatch = mismatch
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69
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70 def setRepMatch(self, repMatch):
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71 self._repMatch = repMatch
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72
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73 def setN(self, N):
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74 self._N = N
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75
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76 def setQGapCount(self, QGapCount):
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77 self._QGapCount = QGapCount
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78
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79 def setQGapBases(self, QGapBases):
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80 self._QGapBases = QGapBases
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81
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82 def setTGapCount(self, TGapCount):
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83 self._TGapCount = TGapCount
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84
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85 def setTGapBases(self, TGapBases):
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86 self._TGapBases = TGapBases
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87
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88 def setStrand(self, strand):
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89 self._strand = strand
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90
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91 def setQName(self, QName):
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92 self._QName = QName
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93
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94 def setQSize(self, QSize):
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95 self._QSize = QSize
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96
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97 def setQStart(self, QStart):
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98 self._QStart = QStart
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99
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100 def setQEnd(self, QEnd):
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101 self._QEnd = QEnd
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102
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103 def setTName(self, TName):
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104 self._TName = TName
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105
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106 def setTSize(self, TSize):
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107 self._TSize = TSize
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108
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109 def setTStart(self, TStart):
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110 self._TStart = TStart
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111
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112 def setTEnd(self, TEnd):
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113 self._TEnd = TEnd
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114
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115 def setBlockCount(self, blockCount):
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116 self._blockCount = blockCount
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117
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118 def setBlockSizes(self, blockSizes):
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119 self._blockSizes = blockSizes
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120
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121 def setQStarts(self, qStarts):
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122 self._qStarts = qStarts
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123
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124 def setTStarts(self, tStarts):
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125 self._tStarts = tStarts
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126
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127 def getMatch(self):
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128 return self._match
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129
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130 def getMismatch(self):
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131 return self._mismatch
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132
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133 def getRepMatch(self):
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134 return self._repMatch
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135
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136 def getN(self):
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137 return self._N
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138
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139 def getQGapCount(self):
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140 return self._QGapCount
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141
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142 def getQGapBases(self):
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143 return self._QGapBases
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144
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145 def getTGapCount(self):
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146 return self._TGapCount
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147
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148 def getTGapBases(self):
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149 return self._TGapBases
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150
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151 def getStrand(self):
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152 return self._strand
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153
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154 def getQName(self):
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155 return self._QName
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156
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157 def getQSize(self):
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158 return self._QSize
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159
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160 def getQStart(self):
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161 return self._QStart
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162
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163 def getQEnd(self):
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164 return self._QEnd
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165
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166 def getTName(self):
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167 return self._TName
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168
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169 def getTSize(self):
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170 return self._TSize
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171
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172 def getTStart(self):
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173 return self._TStart
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174
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175 def getTEnd(self):
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176 return self._TEnd
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177
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178 def getBlockCount(self):
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179 return self._blockCount
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180
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181 def getBlockSizes(self):
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182 return self._blockSizes
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183
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184 def getQStarts(self):
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185 return self._qStarts
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186
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187 def getTStarts(self):
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188 return self._tStarts
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189
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190 def setAttributes(self, lResults, iCurrentLineNumber):
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191 error = False
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192
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193 if lResults[0] != '':
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194 self.setMatch(lResults[0])
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195 else:
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196 sys.stderr.write("WARNING: The field Match is empty in blat file in line %s\n" % iCurrentLineNumber)
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197 error = True
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198
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199 if lResults[1] != '':
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200 self.setMismatch(lResults[1])
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201 else:
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202 sys.stderr.write("WARNING: The field Mismatch is empty in blat file in line %s\n" % iCurrentLineNumber)
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203 error = True
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204
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205 if lResults[2] != '':
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206 self.setRepMatch(lResults[2])
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207 else:
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208 sys.stderr.write("WARNING: The field RepMatch is empty in blat file in line %s\n" % iCurrentLineNumber)
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209 error = True
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210
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211 if lResults[3] != '':
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212 self.setN(lResults[3])
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213 else:
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214 sys.stderr.write("WARNING: The field N is empty in blat file in line %s\n" % iCurrentLineNumber)
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215 error = True
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216
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217 if lResults[4] != '':
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218 self.setQGapCount(lResults[4])
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219 else:
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220 sys.stderr.write("WARNING: The field QGapCount is empty in blat file in line %s\n" % iCurrentLineNumber)
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221 error = True
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222
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223 if lResults[5] != '':
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224 self.setQGapBases(lResults[5])
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225 else:
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226 sys.stderr.write("WARNING: The field QGapBases is empty in blat file in line %s\n" % iCurrentLineNumber)
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227 error = True
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228
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229 if lResults[6] != '':
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230 self.setTGapCount(lResults[6])
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231 else:
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232 sys.stderr.write("WARNING: The field TGapCount is empty in blat file in line %s\n" % iCurrentLineNumber)
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233 error = True
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234
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235 if lResults[7] != '':
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236 self.setTGapBases(lResults[7])
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237 else:
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238 sys.stderr.write("WARNING: The field TGapBases is empty in blat file in line %s\n" % iCurrentLineNumber)
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239 error = True
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240
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241 if lResults[8] != '':
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242 self.setStrand(lResults[8])
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243 else:
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244 sys.stderr.write("WARNING: The field Strand is empty in blat file in line %s\n" % iCurrentLineNumber)
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245 error = True
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246
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247 if lResults[9] != '':
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248 self.setQName(lResults[9])
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249 else:
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250 sys.stderr.write("WARNING: The field QName is empty in blat file in line %s\n" % iCurrentLineNumber)
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251 error = True
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252
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253 if lResults[10] != '':
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254 self.setQSize(lResults[10])
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255 else:
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256 sys.stderr.write("WARNING: The field QSize is empty in blat file in line %s\n" % iCurrentLineNumber)
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257 error = True
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258
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259 if lResults[11] != '':
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260 self.setQStart(lResults[11])
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261 else:
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262 sys.stderr.write("WARNING: The field QStart is empty in blat file in line %s\n" % iCurrentLineNumber)
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263 error = True
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264
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265 if lResults[12] != '':
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266 self.setQEnd(lResults[12])
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267 else:
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268 sys.stderr.write("WARNING: The field QEnd is empty in blat file in line %s\n" % iCurrentLineNumber)
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269 error = True
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270
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271 if lResults[13] != '':
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272 self.setTName(lResults[13])
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273 else:
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274 sys.stderr.write("WARNING: The field TName is empty in blat file in line %s\n" % iCurrentLineNumber)
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275 error = True
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276
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277 if lResults[14] != '':
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278 self.setTSize(lResults[14])
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279 else:
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280 sys.stderr.write("WARNING: The field TSize is empty in blat file in line %s\n" % iCurrentLineNumber)
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281 error = True
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282
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283 if lResults[15] != '':
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284 self.setTStart(lResults[15])
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285 else:
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286 sys.stderr.write("WARNING: The field TStart is empty in blat file in line %s\n" % iCurrentLineNumber)
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287 error = True
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288
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289 if lResults[16] != '':
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290 self.setTEnd(lResults[16])
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291 else:
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292 sys.stderr.write("WARNING: The field TEnd is empty in blat file in line %s\n" % iCurrentLineNumber)
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293 error = True
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294
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295 if lResults[17] != '':
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296 self.setBlockCount(lResults[17])
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297 else:
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298 sys.stderr.write("WARNING: The field BlockCount is empty in blat file in line %s\n" % iCurrentLineNumber)
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299 error = True
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300
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301 if lResults[18] != '':
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302 self.setBlockSizes(lResults[18])
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303 else:
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304 sys.stderr.write("WARNING: The field BlockSizes is empty in blat file in line %s\n" % iCurrentLineNumber)
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305 error = True
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306
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307 if lResults[19] != '':
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308 self.setQStarts(lResults[19])
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309 else:
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310 sys.stderr.write("WARNING: The field QStarts is empty in blat file in line %s\n" % iCurrentLineNumber)
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311 error = True
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312
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313 if lResults[20] != '':
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314 self.setTStarts(lResults[20])
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315 else:
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316 sys.stderr.write("WARNING: The field TStarts is empty in blat file in line %s\n" % iCurrentLineNumber)
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317 error = True
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318
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319 if error == True:
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320 self._setAllToNull()
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321
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322 def setAttributesFromString(self, blatLine, iCurrentLineNumber ="", fieldSeparator ="\t"):
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323 blatLine = blatLine.rstrip()
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324 lBlatLineItem = blatLine.split(fieldSeparator)
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325 if not len(lBlatLineItem) == 21:
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326 sys.stderr.write("WARNING: The line %s is not valid blat line (%s columns -> 21 columns needed)\n" % (iCurrentLineNumber, len(lBlatLineItem)))
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327 else:
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328 self.setAttributes(lBlatLineItem, iCurrentLineNumber)
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329
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330 def _setAllToNull(self):
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331 self._match = ''
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332 self._mismatch = ''
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333 self._repMatch = ''
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334 self._N = ''
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335 self._QGapCount = ''
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336 self._QGapBases = ''
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337 self._TGapCount = ''
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338 self._TGapBases = ''
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339 self._strand = ''
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340 self._QName = ''
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341 self._QSize = ''
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342 self._QStart = ''
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343 self._QEnd = ''
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344 self._TName = ''
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345 self._TSize = ''
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346 self._TStart = ''
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347 self._TEnd = ''
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348 self._blockCount = ''
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349 self._blockSizes = ''
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350 self._qStarts = ''
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351 self._tStarts = '' |
