annotate commons/core/coord/PathUtils.py @ 14:c79b9ae3f65f

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author m-zytnicki
date Fri, 19 Apr 2013 10:13:11 -0400
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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 sys
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34 import copy
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35 from commons.core.coord.Path import Path
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36 from commons.core.coord.SetUtils import SetUtils
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37 from commons.core.coord.Map import Map
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38 from commons.core.coord.AlignUtils import AlignUtils
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39 from commons.core.checker.RepetException import RepetDataException
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40
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41 ## Static methods for the manipulation of Path instances
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42 #
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43 class PathUtils ( object ):
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44
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45 ## Change the identifier of each Set instance in the given list
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46 #
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47 # @param lPaths list of Path instances
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48 # @param newId new identifier
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49 #
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50 def changeIdInList(lPaths, newId):
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51 for iPath in lPaths:
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52 iPath.id = newId
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53
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54 changeIdInList = staticmethod( changeIdInList )
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55
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56
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57 ## Return a list of Set instances containing the query range from a list of Path instances
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58 #
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59 # @param lPaths a list of Path instances
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60 #
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61 def getSetListFromQueries(lPaths):
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62 lSets = []
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63 for iPath in lPaths:
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64 lSets.append( iPath.getSubjectAsSetOfQuery() )
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65 return lSets
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66
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67 getSetListFromQueries = staticmethod( getSetListFromQueries )
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68
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69 #TODO: add tests !!!!
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70 ## Return a list of Set instances containing the query range from a list of Path instances
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71 #
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72 # @param lPaths a list of Path instances
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73 #
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74 @staticmethod
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75 def getSetListFromSubjects(lPaths):
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76 lSets = []
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77 for iPath in lPaths:
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78 lSets.append( iPath.getQuerySetOfSubject() )
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79 return lSets
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80
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81
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82 ## Return a sorted list of Range instances containing the subjects from a list of Path instances
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83 #
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84 # @param lPaths a list of Path instances
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85 # @note meaningful only if all Path instances have same identifier
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86 #
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87 def getRangeListFromSubjects( lPaths ):
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88 lRanges = []
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89 for iPath in lPaths:
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90 lRanges.append( iPath.range_subject )
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91 if lRanges[0].isOnDirectStrand():
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92 return sorted( lRanges, key=lambda iRange: ( iRange.getMin(), iRange.getMax() ) )
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93 else:
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94 return sorted( lRanges, key=lambda iRange: ( iRange.getMax(), iRange.getMin() ) )
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95
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96 getRangeListFromSubjects = staticmethod( getRangeListFromSubjects )
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97
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98
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99 ## Return a tuple with min and max of query coordinates from Path instances in the given list
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100 #
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101 # @param lPaths a list of Path instances
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102 #
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103 def getQueryMinMaxFromPathList(lPaths):
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104 qmin = -1
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105 qmax = -1
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106 for iPath in lPaths:
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107 if qmin == -1:
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108 qmin = iPath.range_query.start
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109 qmin = min(qmin, iPath.range_query.getMin())
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110 qmax = max(qmax, iPath.range_query.getMax())
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111 return (qmin, qmax)
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112
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113 getQueryMinMaxFromPathList = staticmethod( getQueryMinMaxFromPathList )
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114
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115
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116 ## Return a tuple with min and max of subject coordinates from Path instances in the given list
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117 #
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118 # @param lPaths lists of Path instances
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119 #
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120 def getSubjectMinMaxFromPathList(lPaths):
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121 smin = -1
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122 smax = -1
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123 for iPath in lPaths:
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124 if smin == -1:
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125 smin = iPath.range_subject.start
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126 smin = min(smin, iPath.range_subject.getMin())
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127 smax = max(smax, iPath.range_subject.getMax())
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128 return (smin, smax)
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129
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130 getSubjectMinMaxFromPathList = staticmethod( getSubjectMinMaxFromPathList )
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131
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132
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133 ## Return True if the query range of any Path instance from the first list overlaps with the query range of any Path instance from the second list
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134 #
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135 # @param lPaths1: list of Path instances
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136 # @param lPaths2: list of Path instances
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137 # @return boolean
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138 #
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139 def areQueriesOverlappingBetweenPathLists( lPaths1, lPaths2 ):
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140 lSortedPaths1 = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths1 )
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141 lSortedPaths2 = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths2 )
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142 i = 0
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143 j = 0
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144 while i != len(lSortedPaths1):
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145 while j != len(lSortedPaths2):
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146 if not lSortedPaths1[i].range_query.isOverlapping( lSortedPaths2[j].range_query ):
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147 j += 1
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148 else:
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149 return True
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150 i += 1
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151 return False
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152
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153 areQueriesOverlappingBetweenPathLists = staticmethod( areQueriesOverlappingBetweenPathLists )
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154
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155
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156 ## Show Path instances contained in the given list
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157 #
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158 # @param lPaths a list of Path instances
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159 #
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160 def showList(lPaths):
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161 for iPath in lPaths:
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162 iPath.show()
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163
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164 showList = staticmethod( showList )
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165
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166
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167 ## Write Path instances contained in the given list
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168 #
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169 # @param lPaths a list of Path instances
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170 # @param fileName name of the file to write the Path instances
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171 # @param mode the open mode of the file ""w"" or ""a""
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172 #
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173 def writeListInFile(lPaths, fileName, mode="w"):
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174 AlignUtils.writeListInFile(lPaths, fileName, mode)
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175
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176 writeListInFile = staticmethod( writeListInFile )
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177
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178
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179 ## Return new list of Path instances with no duplicate
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180 #
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181 # @param lPaths a list of Path instances
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182 # @param useOnlyCoord boolean if True, check only coordinates and sequence names
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183 # @return lUniqPaths a path instances list
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184 #
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185 def getPathListWithoutDuplicates(lPaths, useOnlyCoord = False):
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186 if len(lPaths) < 2:
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187 return lPaths
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188 lSortedPaths = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier( lPaths )
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189 lUniqPaths = [ lSortedPaths[0] ]
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190 if useOnlyCoord:
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parents:
diff changeset
191 for iPath in lSortedPaths[1:]:
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yufei-luo
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192 if iPath.range_query.start != lUniqPaths[-1].range_query.start \
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yufei-luo
parents:
diff changeset
193 or iPath.range_query.end != lUniqPaths[-1].range_query.end \
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yufei-luo
parents:
diff changeset
194 or iPath.range_query.seqname != lUniqPaths[-1].range_query.seqname \
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yufei-luo
parents:
diff changeset
195 or iPath.range_subject.start != lUniqPaths[-1].range_subject.start \
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yufei-luo
parents:
diff changeset
196 or iPath.range_subject.end != lUniqPaths[-1].range_subject.end \
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yufei-luo
parents:
diff changeset
197 or iPath.range_subject.seqname != lUniqPaths[-1].range_subject.seqname:
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198 lUniqPaths.append( iPath )
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199 else:
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200 for iPath in lSortedPaths[1:]:
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yufei-luo
parents:
diff changeset
201 if iPath != lUniqPaths[-1]:
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yufei-luo
parents:
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202 lUniqPaths.append( iPath )
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203 return lUniqPaths
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204
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205 getPathListWithoutDuplicates = staticmethod( getPathListWithoutDuplicates )
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206
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207
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208 def getPathListWithoutDuplicatesOnQueryCoord(lPaths):
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209 if len(lPaths) < 2:
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210 return lPaths
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211 lSortedPaths = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier( lPaths )
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212 lUniqPaths = [ lSortedPaths[0] ]
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213 for iPath in lSortedPaths[1:]:
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yufei-luo
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214 if iPath.range_query.start != lUniqPaths[-1].range_query.start \
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yufei-luo
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215 or iPath.range_query.end != lUniqPaths[-1].range_query.end \
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yufei-luo
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216 or iPath.range_query.seqname != lUniqPaths[-1].range_query.seqname:
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217 lUniqPaths.append( iPath )
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218 return lUniqPaths
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219
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220 getPathListWithoutDuplicatesOnQueryCoord = staticmethod(getPathListWithoutDuplicatesOnQueryCoord)
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221
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222
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223 ## Split a Path list in several Path lists according to the identifier
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224 #
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225 # @param lPaths a list of Path instances
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226 # @return a dictionary which keys are identifiers and values Path lists
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227 #
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228 def getDictOfListsWithIdAsKey( lPaths ):
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229 dId2PathList = {}
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230 for iPath in lPaths:
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231 if dId2PathList.has_key( iPath.id ):
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232 dId2PathList[ iPath.id ].append( iPath )
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233 else:
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234 dId2PathList[ iPath.id ] = [ iPath ]
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235 return dId2PathList
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236
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237 getDictOfListsWithIdAsKey = staticmethod( getDictOfListsWithIdAsKey )
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238
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239
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240 ## Split a Path file in several Path lists according to the identifier
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241 #
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242 # @param pathFile name of the input Path file
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243 # @return a dictionary which keys are identifiers and values Path lists
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244 #
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245 def getDictOfListsWithIdAsKeyFromFile( pathFile ):
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246 dId2PathList = {}
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247 pathFileHandler = open( pathFile, "r" )
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248 while True:
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249 line = pathFileHandler.readline()
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yufei-luo
parents:
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250 if line == "":
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251 break
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252 iPath = Path()
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253 iPath.setFromString( line )
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yufei-luo
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254 if dId2PathList.has_key( iPath.id ):
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255 dId2PathList[ iPath.id ].append( iPath )
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256 else:
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257 dId2PathList[ iPath.id ] = [ iPath ]
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258 pathFileHandler.close()
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259 return dId2PathList
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260
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261 getDictOfListsWithIdAsKeyFromFile = staticmethod( getDictOfListsWithIdAsKeyFromFile )
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yufei-luo
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262
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263
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264 ## Return a list of Path list(s) obtained while splitting a list of connected Path instances according to another based on query coordinates
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yufei-luo
parents:
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265 #
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266 # @param lToKeep: a list of Path instances to keep (reference)
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yufei-luo
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267 # @param lToUnjoin: a list of Path instances to unjoin
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yufei-luo
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268 # @return: list of Path list(s) (can be empty if one of the input lists is empty)
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269 # @warning: all the path instances in a given list MUST be connected (i.e. same identifier)
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270 # @warning: all the path instances in a given list MUST NOT overlap neither within each other nor with the Path instances of the other list
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yufei-luo
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271 #
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272 def getPathListUnjoinedBasedOnQuery( lToKeep, lToUnjoin ):
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273 lSortedToKeep = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lToKeep )
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yufei-luo
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274 lSortedToUnjoin = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lToUnjoin )
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yufei-luo
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diff changeset
275 if lToUnjoin == []:
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yufei-luo
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276 return []
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yufei-luo
parents:
diff changeset
277 if lToKeep == []:
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yufei-luo
parents:
diff changeset
278 return [ lToUnjoin ]
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yufei-luo
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279
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280 lLists = []
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281 k = 0
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yufei-luo
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diff changeset
282 while k < len(lSortedToKeep):
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yufei-luo
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283 j1 = 0
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yufei-luo
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diff changeset
284 while j1 < len(lSortedToUnjoin) and lSortedToKeep[k].range_query.getMin() > lSortedToUnjoin[j1].range_query.getMax():
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yufei-luo
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285 j1 += 1
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yufei-luo
parents:
diff changeset
286 if j1 == len(lSortedToUnjoin):
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yufei-luo
parents:
diff changeset
287 break
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yufei-luo
parents:
diff changeset
288 if j1 != 0:
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yufei-luo
parents:
diff changeset
289 lLists.append( lSortedToUnjoin[:j1] )
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yufei-luo
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290 del lSortedToUnjoin[:j1]
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yufei-luo
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diff changeset
291 j1 = 0
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yufei-luo
parents:
diff changeset
292 if k+1 == len(lSortedToKeep):
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yufei-luo
parents:
diff changeset
293 break
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yufei-luo
parents:
diff changeset
294 j2 = j1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
295 if j2 < len(lSortedToUnjoin) and lSortedToKeep[k+1].range_query.getMin() > lSortedToUnjoin[j2].range_query.getMax():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
296 while j2 < len(lSortedToUnjoin) and lSortedToKeep[k+1].range_query.getMin() > lSortedToUnjoin[j2].range_query.getMax():
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yufei-luo
parents:
diff changeset
297 j2 += 1
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yufei-luo
parents:
diff changeset
298 lLists.append( lSortedToUnjoin[j1:j2] )
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yufei-luo
parents:
diff changeset
299 del lSortedToUnjoin[j1:j2]
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yufei-luo
parents:
diff changeset
300 k += 1
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yufei-luo
parents:
diff changeset
301
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yufei-luo
parents:
diff changeset
302 if lLists != [] or k == 0:
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yufei-luo
parents:
diff changeset
303 lLists.append( lSortedToUnjoin )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
304 return lLists
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yufei-luo
parents:
diff changeset
305
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parents:
diff changeset
306 getPathListUnjoinedBasedOnQuery = staticmethod( getPathListUnjoinedBasedOnQuery )
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yufei-luo
parents:
diff changeset
307
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yufei-luo
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diff changeset
308
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yufei-luo
parents:
diff changeset
309 ## Return the identity of the Path list, the identity of each instance being weighted by the length of each query range
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310 # All Paths should have the same query and subject.
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yufei-luo
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diff changeset
311 # The Paths are merged using query coordinates only.
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yufei-luo
parents:
diff changeset
312 #
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yufei-luo
parents:
diff changeset
313 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
314 #
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yufei-luo
parents:
diff changeset
315 def getIdentityFromPathList( lPaths, checkSubjects=True ):
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yufei-luo
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diff changeset
316 if len( PathUtils.getListOfDistinctQueryNames( lPaths ) ) > 1:
769e306b7933 Change the repository level.
yufei-luo
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diff changeset
317 msg = "ERROR: try to compute identity from Paths with different queries"
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yufei-luo
parents:
diff changeset
318 sys.stderr.write( "%s\n" % msg )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
319 sys.stderr.flush()
769e306b7933 Change the repository level.
yufei-luo
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diff changeset
320 raise Exception
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
321 if checkSubjects and len( PathUtils.getListOfDistinctSubjectNames( lPaths ) ) > 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
322 msg = "ERROR: try to compute identity from Paths with different subjects"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
323 sys.stderr.write( "%s\n" % msg )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
324 sys.stderr.flush()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
325 raise Exception
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
326 identity = 0
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yufei-luo
parents:
diff changeset
327 lMergedPaths = PathUtils.mergePathsInListUsingQueryCoordsOnly( lPaths )
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yufei-luo
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diff changeset
328 lQuerySets = PathUtils.getSetListFromQueries( lMergedPaths )
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yufei-luo
parents:
diff changeset
329 lMergedQuerySets = SetUtils.mergeSetsInList( lQuerySets )
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yufei-luo
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diff changeset
330 totalLengthOnQry = SetUtils.getCumulLength( lMergedQuerySets )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
331 for iPath in lMergedPaths:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
332 identity += iPath.identity * iPath.getLengthOnQuery()
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yufei-luo
parents:
diff changeset
333 weightedIdentity = identity / float(totalLengthOnQry)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
334 if weightedIdentity < 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
335 msg = "ERROR: weighted identity '%.2f' outside range" % weightedIdentity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
336 sys.stderr.write("%s\n" % msg)
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yufei-luo
parents:
diff changeset
337 sys.stderr.flush()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
338 raise Exception
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
339 elif weightedIdentity > 100:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
340 msg = "ERROR: weighted identity '%.2f' outside range" % weightedIdentity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
341 sys.stderr.write("%s\n" % msg)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
342 sys.stderr.flush()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
343 raise RepetDataException(msg)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
344 return weightedIdentity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
345
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yufei-luo
parents:
diff changeset
346 getIdentityFromPathList = staticmethod( getIdentityFromPathList )
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yufei-luo
parents:
diff changeset
347
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yufei-luo
parents:
diff changeset
348
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yufei-luo
parents:
diff changeset
349 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, and finally their initial order.
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yufei-luo
parents:
diff changeset
350 #
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yufei-luo
parents:
diff changeset
351 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
352 #
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yufei-luo
parents:
diff changeset
353 def getPathListSortedByIncreasingMinQueryThenMaxQuery(lPaths):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
354 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), iPath.getQueryMax() ) )
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yufei-luo
parents:
diff changeset
355
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
356 getPathListSortedByIncreasingMinQueryThenMaxQuery = staticmethod( getPathListSortedByIncreasingMinQueryThenMaxQuery )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
357
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yufei-luo
parents:
diff changeset
358
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yufei-luo
parents:
diff changeset
359 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, then their identifier, and finally their initial order.
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yufei-luo
parents:
diff changeset
360 #
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yufei-luo
parents:
diff changeset
361 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
362 #
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yufei-luo
parents:
diff changeset
363 def getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier(lPaths):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
364 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), iPath.getQueryMax(), iPath.getIdentifier() ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
365
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
366 getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier = staticmethod( getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
367
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
368
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
369 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, then the min of the subject, then the max of the subject and finally their initial order.
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yufei-luo
parents:
diff changeset
370 #
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yufei-luo
parents:
diff changeset
371 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
372 #
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yufei-luo
parents:
diff changeset
373 @staticmethod
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yufei-luo
parents:
diff changeset
374 def getPathListSortedByIncreasingMinQueryThenMaxQueryThenMinSubjectThenMaxSubject(lPaths):
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yufei-luo
parents:
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375 return sorted(lPaths, key=lambda iPath: (iPath.getQueryMin(), iPath.getQueryMax(), iPath.getSubjectMin(), iPath.getSubjectMax()))
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yufei-luo
parents:
diff changeset
376
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
377
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yufei-luo
parents:
diff changeset
378 ## Return a list of the distinct identifiers
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yufei-luo
parents:
diff changeset
379 #
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yufei-luo
parents:
diff changeset
380 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
381 #
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yufei-luo
parents:
diff changeset
382 def getListOfDistinctIdentifiers( lPaths ):
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yufei-luo
parents:
diff changeset
383 sDistinctIdentifiers = set()
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yufei-luo
parents:
diff changeset
384 for iPath in lPaths:
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yufei-luo
parents:
diff changeset
385 sDistinctIdentifiers.add(iPath.id)
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yufei-luo
parents:
diff changeset
386 return list(sDistinctIdentifiers)
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yufei-luo
parents:
diff changeset
387
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yufei-luo
parents:
diff changeset
388 getListOfDistinctIdentifiers = staticmethod( getListOfDistinctIdentifiers )
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yufei-luo
parents:
diff changeset
389
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yufei-luo
parents:
diff changeset
390
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yufei-luo
parents:
diff changeset
391 ## Return a list of the distinct query names present in the collection
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yufei-luo
parents:
diff changeset
392 #
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yufei-luo
parents:
diff changeset
393 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
394 #
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yufei-luo
parents:
diff changeset
395 def getListOfDistinctQueryNames( lPaths ):
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yufei-luo
parents:
diff changeset
396 sDistinctQueryNames = set()
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yufei-luo
parents:
diff changeset
397 for iPath in lPaths:
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yufei-luo
parents:
diff changeset
398 sDistinctQueryNames.add(iPath.range_query.seqname)
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yufei-luo
parents:
diff changeset
399 return list(sDistinctQueryNames)
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yufei-luo
parents:
diff changeset
400
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yufei-luo
parents:
diff changeset
401 getListOfDistinctQueryNames = staticmethod( getListOfDistinctQueryNames )
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yufei-luo
parents:
diff changeset
402
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yufei-luo
parents:
diff changeset
403
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yufei-luo
parents:
diff changeset
404 ## Return a list of the distinct subject names present in the collection
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yufei-luo
parents:
diff changeset
405 #
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yufei-luo
parents:
diff changeset
406 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
407 #
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yufei-luo
parents:
diff changeset
408 def getListOfDistinctSubjectNames( lPaths ):
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yufei-luo
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409 sDistinctSubjectNames = set()
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yufei-luo
parents:
diff changeset
410 for iPath in lPaths:
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yufei-luo
parents:
diff changeset
411 sDistinctSubjectNames.add(iPath.range_subject.seqname)
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yufei-luo
parents:
diff changeset
412 return list(sDistinctSubjectNames)
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yufei-luo
parents:
diff changeset
413
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yufei-luo
parents:
diff changeset
414 getListOfDistinctSubjectNames = staticmethod( getListOfDistinctSubjectNames )
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yufei-luo
parents:
diff changeset
415
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yufei-luo
parents:
diff changeset
416
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yufei-luo
parents:
diff changeset
417 ## Return a list of lists containing query coordinates of the connections sorted in increasing order.
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yufei-luo
parents:
diff changeset
418 #
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yufei-luo
parents:
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419 # @param lConnectedPaths: list of Path instances having the same identifier
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yufei-luo
parents:
diff changeset
420 # @param minLength: threshold below which connections are not reported (default= 0 bp)
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yufei-luo
parents:
diff changeset
421 # @note: return only connections longer than threshold
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yufei-luo
parents:
diff changeset
422 # @note: if coordinate on query ends at 100, return 101
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yufei-luo
parents:
diff changeset
423 # @warning: Path instances MUST be sorted in increasing order according to query coordinates
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yufei-luo
parents:
diff changeset
424 # @warning: Path instances MUST be on direct query strand (and maybe on reverse subject strand)
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yufei-luo
parents:
diff changeset
425 #
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yufei-luo
parents:
diff changeset
426 def getListOfJoinCoordinatesOnQuery(lConnectedPaths, minLength=0):
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yufei-luo
parents:
diff changeset
427 lJoinCoordinates = []
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yufei-luo
parents:
diff changeset
428 for i in xrange(1,len(lConnectedPaths)):
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yufei-luo
parents:
diff changeset
429 startJoin = lConnectedPaths[i-1].range_query.end
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yufei-luo
parents:
diff changeset
430 endJoin = lConnectedPaths[i].range_query.start
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yufei-luo
parents:
diff changeset
431 if endJoin - startJoin + 1 > minLength:
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yufei-luo
parents:
diff changeset
432 lJoinCoordinates.append( [ startJoin + 1, endJoin - 1 ] )
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yufei-luo
parents:
diff changeset
433 return lJoinCoordinates
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yufei-luo
parents:
diff changeset
434
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yufei-luo
parents:
diff changeset
435 getListOfJoinCoordinatesOnQuery = staticmethod( getListOfJoinCoordinatesOnQuery )
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yufei-luo
parents:
diff changeset
436
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yufei-luo
parents:
diff changeset
437
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yufei-luo
parents:
diff changeset
438 ## Return the length on the query of all Path instance in the given list
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yufei-luo
parents:
diff changeset
439 #
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yufei-luo
parents:
diff changeset
440 # @param lPaths list of Path instances
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yufei-luo
parents:
diff changeset
441 # @note overlapping ranges are not summed but truncated.
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yufei-luo
parents:
diff changeset
442 #
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yufei-luo
parents:
diff changeset
443 def getLengthOnQueryFromPathList( lPaths ):
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yufei-luo
parents:
diff changeset
444 lSets = PathUtils.getSetListFromQueries( lPaths )
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yufei-luo
parents:
diff changeset
445 lMergedSets = SetUtils.mergeSetsInList( lSets )
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yufei-luo
parents:
diff changeset
446 length = SetUtils.getCumulLength( lMergedSets )
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yufei-luo
parents:
diff changeset
447 return length
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yufei-luo
parents:
diff changeset
448
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yufei-luo
parents:
diff changeset
449 getLengthOnQueryFromPathList = staticmethod( getLengthOnQueryFromPathList )
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yufei-luo
parents:
diff changeset
450
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yufei-luo
parents:
diff changeset
451
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yufei-luo
parents:
diff changeset
452 ## Convert a Path file into an Align file
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yufei-luo
parents:
diff changeset
453 #
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yufei-luo
parents:
diff changeset
454 # @param pathFile: name of the input Path file
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yufei-luo
parents:
diff changeset
455 # @param alignFile: name of the output Align file
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yufei-luo
parents:
diff changeset
456 #
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yufei-luo
parents:
diff changeset
457 def convertPathFileIntoAlignFile(pathFile, alignFile):
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yufei-luo
parents:
diff changeset
458 pathFileHandler = open( pathFile, "r" )
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yufei-luo
parents:
diff changeset
459 alignFileHandler = open( alignFile, "w" )
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yufei-luo
parents:
diff changeset
460 iPath = Path()
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yufei-luo
parents:
diff changeset
461 while True:
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yufei-luo
parents:
diff changeset
462 line = pathFileHandler.readline()
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yufei-luo
parents:
diff changeset
463 if line == "":
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yufei-luo
parents:
diff changeset
464 break
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yufei-luo
parents:
diff changeset
465 iPath.setFromString( line )
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yufei-luo
parents:
diff changeset
466 iAlign = iPath.getAlignInstance()
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yufei-luo
parents:
diff changeset
467 iAlign.write( alignFileHandler )
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yufei-luo
parents:
diff changeset
468 pathFileHandler.close()
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yufei-luo
parents:
diff changeset
469 alignFileHandler.close()
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yufei-luo
parents:
diff changeset
470
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yufei-luo
parents:
diff changeset
471 convertPathFileIntoAlignFile = staticmethod( convertPathFileIntoAlignFile )
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yufei-luo
parents:
diff changeset
472
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yufei-luo
parents:
diff changeset
473 #TODO: duplicated method => to rename with the name of the next method (which is called) ?
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yufei-luo
parents:
diff changeset
474 ## Convert a Path File into a Map file with query coordinates only
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yufei-luo
parents:
diff changeset
475 #
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yufei-luo
parents:
diff changeset
476 # @param pathFile: name of the input Path file
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yufei-luo
parents:
diff changeset
477 # @param mapFile: name of the output Map file
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yufei-luo
parents:
diff changeset
478 #
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yufei-luo
parents:
diff changeset
479 def convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, mapFile ):
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yufei-luo
parents:
diff changeset
480 pathFileHandler = open( pathFile, "r" )
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yufei-luo
parents:
diff changeset
481 mapFileHandler = open( mapFile, "w" )
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yufei-luo
parents:
diff changeset
482 p = Path()
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yufei-luo
parents:
diff changeset
483 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
484 line = pathFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
485 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
486 break
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yufei-luo
parents:
diff changeset
487 p.reset()
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yufei-luo
parents:
diff changeset
488 p.setFromTuple( line.split("\t") )
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yufei-luo
parents:
diff changeset
489 p.writeSubjectAsMapOfQuery( mapFileHandler )
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yufei-luo
parents:
diff changeset
490 pathFileHandler.close()
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yufei-luo
parents:
diff changeset
491 mapFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
492
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
493 convertPathFileIntoMapFileWithQueryCoordsOnly = staticmethod( convertPathFileIntoMapFileWithQueryCoordsOnly )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
494
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
495
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
496 ## for each line of a given Path file, write the coordinates of the subject on the query as one line in a Map file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
497 #
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yufei-luo
parents:
diff changeset
498 # @param pathFile: name of the input Path file
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yufei-luo
parents:
diff changeset
499 # @param mapFile: name of the output Map file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
500 #
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yufei-luo
parents:
diff changeset
501 def convertPathFileIntoMapFileWithSubjectsOnQueries( pathFile, mapFile ):
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yufei-luo
parents:
diff changeset
502 PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, mapFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
503 convertPathFileIntoMapFileWithSubjectsOnQueries = staticmethod( convertPathFileIntoMapFileWithSubjectsOnQueries )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
504
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
505
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
506 ## Merge matches on queries
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
507 #
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yufei-luo
parents:
diff changeset
508 # @param inFile: name of the input Path file
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yufei-luo
parents:
diff changeset
509 # @param outFile: name of the output Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
510 #
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yufei-luo
parents:
diff changeset
511 def mergeMatchesOnQueries(inFile, outFile):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
512 mapFile = "%s.map" % ( inFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
513 PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( inFile, mapFile )
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yufei-luo
parents:
diff changeset
514 cmd = "mapOp"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
515 cmd += " -q %s" % ( mapFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
516 cmd += " -m"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
517 cmd += " 2>&1 > /dev/null"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
518 exitStatus = os.system( cmd )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
519 if exitStatus != 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
520 print "ERROR: mapOp returned %i" % ( exitStatus )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
521 sys.exit(1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
522 os.remove( mapFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
523 mergeFile = "%s.merge" % ( mapFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
524 mergeFileHandler = open( mergeFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
525 outFileHandler = open( outFile, "w" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
526 m = Map()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
527 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
528 line = mergeFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
529 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
530 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
531 m.reset()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
532 m.setFromString( line, "\t" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
533 m.writeAsQueryOfPath( outFileHandler )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
534 mergeFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
535 os.remove( mergeFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
536 outFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
537
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
538 mergeMatchesOnQueries = staticmethod( mergeMatchesOnQueries )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
539
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
540
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
541 ## Filter chains of Path(s) which length is below a given threshold
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
542 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
543 # @param lPaths: list of Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
544 # @param minLengthChain: minimum length of a chain to be kept
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
545 # @note: a chain may contain a single Path instance
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
546 # @return: a list of Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
547 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
548 def filterPathListOnChainLength( lPaths, minLengthChain ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
549 lFilteredPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
550 dPathnum2Paths = PathUtils.getDictOfListsWithIdAsKey( lPaths )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
551 for pathnum in dPathnum2Paths.keys():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
552 length = PathUtils.getLengthOnQueryFromPathList( dPathnum2Paths[ pathnum ] )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
553 if length >= minLengthChain:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
554 lFilteredPaths += dPathnum2Paths[ pathnum ]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
555 return lFilteredPaths
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
556
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
557 filterPathListOnChainLength = staticmethod( filterPathListOnChainLength )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
558
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
559
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
560 ## Return a Path list from a Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
561 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
562 # @param pathFile string name of a Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
563 # @return a list of Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
564 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
565 def getPathListFromFile( pathFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
566 lPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
567 pathFileHandler = open( pathFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
568 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
569 line = pathFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
570 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
571 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
572 iPath = Path()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
573 iPath.setFromString( line )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
574 lPaths.append( iPath )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
575 pathFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
576 return lPaths
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
577
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
578 getPathListFromFile = staticmethod( getPathListFromFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
579
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
580
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
581 ## Convert a chain into a 'pathrange'
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
582 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
583 # @param lPaths a list of Path instances with the same identifier
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
584 # @note: the min and max of each Path is used
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
585 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
586 def convertPathListToPathrange( lPaths ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
587 if len(lPaths) == 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
588 return
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
589 if len(lPaths) == 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
590 return lPaths[0]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
591 iPathrange = copy.deepcopy( lPaths[0] )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
592 iPathrange.identity = lPaths[0].identity * lPaths[0].getLengthOnQuery()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
593 cumulQueryLength = iPathrange.getLengthOnQuery()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
594 for iPath in lPaths[1:]:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
595 if iPath.id != iPathrange.id:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
596 msg = "ERROR: two Path instances in the chain have different identifiers"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
597 sys.stderr.write( "%s\n" % ( msg ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
598 sys.exit(1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
599 if iPathrange.range_subject.isOnDirectStrand() != iPath.range_subject.isOnDirectStrand():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
600 msg = "ERROR: two Path instances in the chain are on different strands"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
601 sys.stderr.write( "%s\n" % ( msg ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
602 sys.exit(1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
603 iPathrange.range_query.start = min( iPathrange.range_query.start, iPath.range_query.start )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
604 iPathrange.range_query.end = max( iPathrange.range_query.end, iPath.range_query.end )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
605 if iPathrange.range_subject.isOnDirectStrand():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
606 iPathrange.range_subject.start = min( iPathrange.range_subject.start, iPath.range_subject.start )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
607 iPathrange.range_subject.end = max( iPathrange.range_subject.end, iPath.range_subject.end )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
608 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
609 iPathrange.range_subject.start = max( iPathrange.range_subject.start, iPath.range_subject.start )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
610 iPathrange.range_subject.end = min( iPathrange.range_subject.end, iPath.range_subject.end )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
611 iPathrange.e_value = min( iPathrange.e_value, iPath.e_value )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
612 iPathrange.score += iPath.score
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
613 iPathrange.identity += iPath.identity * iPath.getLengthOnQuery()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
614 cumulQueryLength += iPath.getLengthOnQuery()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
615 iPathrange.identity = iPathrange.identity / float(cumulQueryLength)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
616 return iPathrange
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
617
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
618 convertPathListToPathrange = staticmethod( convertPathListToPathrange )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
619
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
620
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
621 ## Convert a Path file into an Align file via 'pathrange'
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
622 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
623 # @param pathFile: name of the input Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
624 # @param alignFile: name of the output Align file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
625 # @param verbose integer verbosity level
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
626 # @note: the min and max of each Path is used
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
627 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
628 def convertPathFileIntoAlignFileViaPathrange( pathFile, alignFile, verbose=0 ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
629 lPaths = PathUtils.getPathListFromFile( pathFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
630 dId2PathList = PathUtils.getDictOfListsWithIdAsKey( lPaths )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
631 lIds = dId2PathList.keys()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
632 lIds.sort()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
633 if verbose > 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
634 msg = "number of chains: %i" % ( len(lIds) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
635 sys.stdout.write( "%s\n" % ( msg ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
636 sys.stdout.flush()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
637 alignFileHandler = open( alignFile, "w" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
638 for identifier in lIds:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
639 iPath = PathUtils.convertPathListToPathrange( dId2PathList[ identifier ] )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
640 iAlign = iPath.getAlignInstance()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
641 iAlign.write( alignFileHandler )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
642 alignFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
643
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
644 convertPathFileIntoAlignFileViaPathrange = staticmethod( convertPathFileIntoAlignFileViaPathrange )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
645
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
646
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
647 ## Split a list of Path instances according to the name of the query
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
648 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
649 # @param lInPaths list of align instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
650 # @return lOutPathLists list of align instances lists
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
651 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
652 def splitPathListByQueryName( lInPaths ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
653 lInSortedPaths = sorted( lInPaths, key=lambda o: o.range_query.seqname )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
654 lOutPathLists = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
655 if len(lInSortedPaths) != 0 :
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
656 lPathsForCurrentQuery = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
657 previousQuery = lInSortedPaths[0].range_query.seqname
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
658 for iPath in lInSortedPaths :
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
659 currentQuery = iPath.range_query.seqname
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
660 if previousQuery != currentQuery :
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
661 lOutPathLists.append( lPathsForCurrentQuery )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
662 previousQuery = currentQuery
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
663 lPathsForCurrentQuery = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
664 lPathsForCurrentQuery.append( iPath )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
665
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
666 lOutPathLists.append(lPathsForCurrentQuery)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
667
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
668 return lOutPathLists
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
669
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
670 splitPathListByQueryName = staticmethod( splitPathListByQueryName )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
671
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
672
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
673 ## Create an Path file from each list of Path instances in the input list
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
674 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
675 # @param lPathList list of lists with Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
676 # @param pattern string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
677 # @param dirName string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
678 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
679 def createPathFiles( lPathList, pattern, dirName="" ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
680 nbFiles = len(lPathList)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
681 countFile = 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
682 if dirName != "" :
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
683 if dirName[-1] != "/":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
684 dirName = dirName + '/'
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
685 os.mkdir( dirName )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
686
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
687 for lPath in lPathList:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
688 fileName = dirName + pattern + "_%s.path" % ( str(countFile).zfill( len(str(nbFiles)) ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
689 PathUtils.writeListInFile( lPath, fileName )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
690 countFile += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
691
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
692 createPathFiles = staticmethod( createPathFiles )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
693
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
694
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
695 ## Return a list of Path instances sorted in increasing order according to the min, then the inverse of the query length, and finally their initial order
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
696 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
697 # @param lPaths: list of Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
698 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
699 def getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
700 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), 1 / float(iPath.getLengthOnQuery()) ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
701
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
702 getPathListSortedByIncreasingQueryMinThenInvQueryLength = staticmethod( getPathListSortedByIncreasingQueryMinThenInvQueryLength )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
703
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
704
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
705 ## Merge all overlapping Path instances in a list without considering the identifiers
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
706 # Start by sorting the Path instances by their increasing min coordinate
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
707 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
708 # @return: a new list with the merged Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
709 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
710 def mergePathsInList( lPaths ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
711 lMergedPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
712 if len(lPaths)==0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
713 return lMergedPaths
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
714
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
715 lSortedPaths = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
716
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
717 prev_count = 0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
718 for iPath in lSortedPaths[0:]:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
719 if prev_count != len(lSortedPaths):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
720 for i in lSortedPaths[ prev_count + 1: ]:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
721 if iPath.isOverlapping( i ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
722 iPath.merge( i )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
723 isAlreadyInList = False
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
724 for newPath in lMergedPaths:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
725 if newPath.isOverlapping( iPath ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
726 isAlreadyInList = True
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
727 newPath.merge( iPath )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
728 lMergedPaths [ lMergedPaths.index( newPath ) ] = newPath
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
729 if not isAlreadyInList:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
730 lMergedPaths.append( iPath )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
731 prev_count += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
732 return lMergedPaths
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
733
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
734 mergePathsInList = staticmethod( mergePathsInList )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
735
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
736
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
737 ## Merge all overlapping Path instances in a list without considering if subjects are overlapping.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
738 # Start by sorting the Path instances by their increasing min coordinate.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
739 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
740 # @return: a new list with the merged Path instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
741 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
742 def mergePathsInListUsingQueryCoordsOnly( lPaths ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
743 lMergedPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
744 if len(lPaths)==0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
745 return lMergedPaths
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
746
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
747 lSortedPaths = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
748
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
749 prev_count = 0
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yufei-luo
parents:
diff changeset
750 for iPath in lSortedPaths[0:]:
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yufei-luo
parents:
diff changeset
751 if prev_count != len(lSortedPaths):
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yufei-luo
parents:
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752 for i in lSortedPaths[ prev_count + 1: ]:
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yufei-luo
parents:
diff changeset
753 if iPath.isQueryOverlapping( i ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
754 iPath.merge( i )
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yufei-luo
parents:
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755 isAlreadyInList = False
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yufei-luo
parents:
diff changeset
756 for newPath in lMergedPaths:
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yufei-luo
parents:
diff changeset
757 if newPath.isQueryOverlapping( iPath ):
769e306b7933 Change the repository level.
yufei-luo
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diff changeset
758 isAlreadyInList = True
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yufei-luo
parents:
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759 newPath.merge( iPath )
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yufei-luo
parents:
diff changeset
760 lMergedPaths [ lMergedPaths.index( newPath ) ] = newPath
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yufei-luo
parents:
diff changeset
761 if not isAlreadyInList:
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yufei-luo
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diff changeset
762 lMergedPaths.append( iPath )
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yufei-luo
parents:
diff changeset
763 prev_count += 1
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yufei-luo
parents:
diff changeset
764 return lMergedPaths
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yufei-luo
parents:
diff changeset
765
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yufei-luo
parents:
diff changeset
766 mergePathsInListUsingQueryCoordsOnly = staticmethod( mergePathsInListUsingQueryCoordsOnly )
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yufei-luo
parents:
diff changeset
767
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yufei-luo
parents:
diff changeset
768
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
769 ## Convert a Path file into a GFF file
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yufei-luo
parents:
diff changeset
770 #
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yufei-luo
parents:
diff changeset
771 # @param pathFile: name of the input Path file
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yufei-luo
parents:
diff changeset
772 # @param gffFile: name of the output GFF file
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yufei-luo
parents:
diff changeset
773 # @param source: source to write in the GFF file (column 2)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
774 #
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yufei-luo
parents:
diff changeset
775 # @note the 'path' query is supposed to correspond to the 'gff' first column
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yufei-luo
parents:
diff changeset
776 #
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yufei-luo
parents:
diff changeset
777 def convertPathFileIntoGffFile( pathFile, gffFile, source="REPET", verbose=0 ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
778 dId2PathList = PathUtils.getDictOfListsWithIdAsKeyFromFile( pathFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
779 if verbose > 0:
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yufei-luo
parents:
diff changeset
780 msg = "number of chains: %i" % ( len(dId2PathList.keys()) )
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yufei-luo
parents:
diff changeset
781 sys.stdout.write( "%s\n" % msg )
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yufei-luo
parents:
diff changeset
782 sys.stdout.flush()
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yufei-luo
parents:
diff changeset
783 gffFileHandler = open( gffFile, "w" )
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yufei-luo
parents:
diff changeset
784 for id in dId2PathList.keys():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
785 if len( dId2PathList[ id ] ) == 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
786 iPath = dId2PathList[ id ][0]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
787 string = iPath.toStringAsGff( ID="%i" % iPath.getIdentifier(),
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
788 source=source )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
789 gffFileHandler.write( "%s\n" % string )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
790 else:
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yufei-luo
parents:
diff changeset
791 iPathrange = PathUtils.convertPathListToPathrange( dId2PathList[ id ] )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
792 string = iPathrange.toStringAsGff( ID="ms%i" % iPathrange.getIdentifier(),
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
793 source=source )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
794 gffFileHandler.write( "%s\n" % string )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
795 count = 0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
796 for iPath in dId2PathList[ id ]:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
797 count += 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
798 string = iPath.toStringAsGff( type="match_part",
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
799 ID="mp%i-%i" % ( iPath.getIdentifier(), count ),
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
800 Parent="ms%i" % iPathrange.getIdentifier(),
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
801 source=source )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
802 gffFileHandler.write( "%s\n" % string )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
803 gffFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
804
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
805 convertPathFileIntoGffFile = staticmethod( convertPathFileIntoGffFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
806
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
807
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
808 ## Convert a Path file into a Set file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
809 # replace old parser.pathrange2set
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
810 # @param pathFile: name of the input Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
811 # @param setFile: name of the output Set file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
812 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
813 def convertPathFileIntoSetFile( pathFile, setFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
814 pathFileHandler = open( pathFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
815 setFileHandler = open( setFile, "w" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
816 iPath = Path()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
817 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
818 line = pathFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
819 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
820 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
821 iPath.setFromString( line )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
822 iSet = iPath.getSubjectAsSetOfQuery()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
823 iSet.write( setFileHandler )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
824 pathFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
825 setFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
826
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
827 convertPathFileIntoSetFile = staticmethod( convertPathFileIntoSetFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
828
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
829 ## Write Path File without duplicated Path (same query, same subject and same coordinate)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
830 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
831 # @param inputFile: name of the input Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
832 # @param outputFile: name of the output Path file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
833 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
834 def removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName(inputFile, outputFile):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
835 f = open(inputFile, "r")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
836 line = f.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
837 previousQuery = ""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
838 previousSubject = ""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
839 lPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
840 while line:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
841 iPath = Path()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
842 iPath.setFromString(line)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
843 query = iPath.getQueryName()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
844 subject = iPath.getSubjectName()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
845 if (query != previousQuery or subject != previousSubject) and lPaths != []:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
846 lPathsWithoutDuplicate = PathUtils.getPathListWithoutDuplicatesOnQueryCoord(lPaths)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
847 PathUtils.writeListInFile(lPathsWithoutDuplicate, outputFile, "a")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
848 lPaths = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
849 lPaths.append(iPath)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
850 previousQuery = query
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
851 previousSubject = subject
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
852 line = f.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
853 lPathsWithoutDuplicate = PathUtils.getPathListWithoutDuplicatesOnQueryCoord(lPaths)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
854 PathUtils.writeListInFile(lPathsWithoutDuplicate, outputFile, "a")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
855 f.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
856 removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName = staticmethod(removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
857
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
858