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1 from pyRepet.coord.Map import Map
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2 import commons.core.sql.TablePathAdaptator
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3
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4
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5 ## Connect overlapping chunks in a single fragment
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6 #
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7 class PathChunkConnector( object):
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8
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9 def __init__(self, mapFileName, db, table, verbose):
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10
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11 self._verbose = verbose
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12 self._chunk = self._getChunkDictFromMapFileForConnectPathChunks( mapFileName )
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13 self._tablePathAdaptator = commons.core.sql.TablePathAdaptator.TablePathAdaptator( db, table )
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14
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15 def run (self):
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16 for num_chunk in xrange(1,len(self._chunk.keys())):
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17 chunkName = "chunk"+str(num_chunk)
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18 if self._verbose > 1:
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19 print chunkName
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20 next_chunkName="chunk"+str(num_chunk+1)
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21
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22 if next_chunkName not in self._chunk.keys():
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23 break
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24
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25 start=self._chunk[chunkName][2]
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26 end=self._chunk[next_chunkName][1]
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27
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28 if self._chunk[chunkName][0] == self._chunk[next_chunkName][0]:
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29 lpath=self._tablePathAdaptator.getPathListIncludedInQueryCoord(self._chunk[chunkName][0],start,end)
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30
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31 if self._verbose > 1:
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32 print "----------"
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33
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34 lpath.sort()
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35 chg_path_id={}
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36 pathnum_to_ins=[]
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37 pathnum_to_del=[]
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38
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39 self._createDirectAndReversePaths(lpath)
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40
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41 self._mergeDirectPaths(chg_path_id, pathnum_to_ins, pathnum_to_del)
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42
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43 if self._verbose > 1:
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44 print "..........."
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45
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46 self._mergeReversePaths(chg_path_id, pathnum_to_ins, pathnum_to_del)
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47
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48 if self._verbose > 1:
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49 print "..........."
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50 print pathnum_to_del
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51
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52 self._tablePathAdaptator.deleteFromIdList(pathnum_to_del)
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53
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54 if self._verbose > 1:
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55 print pathnum_to_ins
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56
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57 self._tablePathAdaptator.deleteFromIdList(pathnum_to_ins)
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58
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59 self._insertDirectPaths(chg_path_id, pathnum_to_ins)
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60
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61 self._insertReversePaths(chg_path_id, pathnum_to_ins)
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62
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63
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64 def _createDirectAndReversePaths(self, lpath):
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65 self._dpath = []
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66 self._rpath = []
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67 for i in lpath:
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68 if i.range_query.isOnDirectStrand() and i.range_subject.isOnDirectStrand():
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69 self._dpath.append(i)
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70 else:
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71 self._rpath.append(i)
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72
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73 def _insertDirectPaths (self, chg_path_id, pathnum_to_ins):
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74 self._insertPaths(chg_path_id, pathnum_to_ins, self._dpath)
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75
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76 def _insertReversePaths (self, chg_path_id, pathnum_to_ins):
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77 self._insertPaths(chg_path_id, pathnum_to_ins, self._rpath)
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78
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79 def _insertPaths(self, chg_path_id, pathnum_to_ins, paths2Insert):
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80 for i in paths2Insert:
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81 if chg_path_id.has_key(i.id):
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82 i.id = chg_path_id[i.id]
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83
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84 if self._verbose > 1:
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85 i.show()
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86
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87 if i.id in pathnum_to_ins:
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88 self._tablePathAdaptator.insert(i)
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89 if self._verbose > 1:
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90 print "--> inserted!"
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91
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92 if self._verbose > 1:
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93 print "=========="
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94
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95 def _mergeDirectPaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del):
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96 self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._dpath)
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97
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98 def _mergeReversePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del):
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99 self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._rpath)
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100
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101 def _mergePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del, dpath):
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102 x = 0
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103 while x < len(dpath) - 1:
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104 x = x + 1
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105 if self._verbose > 1:
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106 print "++++"
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107 dpath[x - 1].show()
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108 dpath[x].show()
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109
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110 if dpath[x - 1].canMerge(dpath[x]):
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111 chg_path_id[dpath[x].id] = dpath[x - 1].id
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112 if dpath[x - 1].id not in pathnum_to_ins:
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113 pathnum_to_ins.append(dpath[x - 1].id)
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114
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115 if dpath[x].id not in pathnum_to_del:
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116 pathnum_to_del.append(dpath[x].id)
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117
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118 dpath[x - 1].merge(dpath[x])
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119 del dpath[x]
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120 x = x - 1
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121 if self._verbose > 1:
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122 print "--> merged"
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123
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124 def _getChunkDictFromMapFileForConnectPathChunks(self, mapFileName):
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125 mapDict = {}
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126 mapFile = open(mapFileName)
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127 mapInstance = Map()
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128 while True:
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129 if not mapInstance.read(mapFile):
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130 break
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131 mapDict[mapInstance.name] = (mapInstance.seqname, mapInstance.start, mapInstance.end)
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132
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133 mapFile.close()
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134 return mapDict
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