Exemple #1
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 def sameCoordinates(self, pairwiseAlignment):
     return self.contig1 == pairwiseAlignment.contig1 and \
     self.start1 == pairwiseAlignment.start1 and \
     self.end1 == pairwiseAlignment.end1 and \
     self.strand1 == pairwiseAlignment.strand1 and \
     self.contig2 == pairwiseAlignment.contig2 and \
     self.start2 == pairwiseAlignment.start2 and \
     self.end2 == pairwiseAlignment.end2 and \
     self.strand2 == pairwiseAlignment.strand2 and \
     close(self.score, pairwiseAlignment.score, 0.001)
Exemple #2
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 def __eq__(self, pairwiseAlignment):
     if pairwiseAlignment is None:
         return False
     return self.contig1 == pairwiseAlignment.contig1 and \
     self.start1 == pairwiseAlignment.start1 and \
     self.end1 == pairwiseAlignment.end1 and \
     self.strand1 == pairwiseAlignment.strand1 and \
     self.contig2 == pairwiseAlignment.contig2 and \
     self.start2 == pairwiseAlignment.start2 and \
     self.end2 == pairwiseAlignment.end2 and \
     self.strand2 == pairwiseAlignment.strand2 and \
     close(self.score, pairwiseAlignment.score, 0.001) and \
     self.operationList == pairwiseAlignment.operationList
Exemple #3
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 def __eq__(self, pairwiseAlignment):
     if pairwiseAlignment is None:
         return False
     return self.contig1 == pairwiseAlignment.contig1 and \
     self.start1 == pairwiseAlignment.start1 and \
     self.end1 == pairwiseAlignment.end1 and \
     self.strand1 == pairwiseAlignment.strand1 and \
     self.contig2 == pairwiseAlignment.contig2 and \
     self.start2 == pairwiseAlignment.start2 and \
     self.end2 == pairwiseAlignment.end2 and \
     self.strand2 == pairwiseAlignment.strand2 and \
     close(self.score, pairwiseAlignment.score, 0.001) and \
     self.operationList == pairwiseAlignment.operationList
Exemple #4
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 def testRemodelTreeRemovingRoot(self):
     for test in xrange(0, self.testNo):
         binaryTree = getRandomTree()
         binaryTree_depthFirstNumbers(binaryTree) 
         node = getRandomLeafNode(binaryTree)
         remodTree = remodelTreeRemovingRoot(binaryTree, node.traversalID.mid)
         print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
         binaryTree_depthFirstNumbers(remodTree)
         distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
         d = getDistancesBetweenLeaves(binaryTree)
         d2 = getDistancesBetweenLeaves(remodTree)
         print d
         print d2
         for key in d2:
             assert close(d2[key], d[key], 0.0001)
Exemple #5
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 def testRemodelTreeRemovingRoot(self):
     for test in xrange(0, self.testNo):
         binaryTree = getRandomTree()
         binaryTree_depthFirstNumbers(binaryTree)
         node = getRandomLeafNode(binaryTree)
         remodTree = remodelTreeRemovingRoot(binaryTree,
                                             node.traversalID.mid)
         print "test", test, printBinaryTree(
             binaryTree,
             True), printBinaryTree(node,
                                    True), printBinaryTree(remodTree, True)
         binaryTree_depthFirstNumbers(remodTree)
         distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
         d = getDistancesBetweenLeaves(binaryTree)
         d2 = getDistancesBetweenLeaves(remodTree)
         print d
         print d2
         for key in d2:
             assert close(d2[key], d[key], 0.0001)
Exemple #6
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 def __eq__(self, op):
     if op is None:
         return False
     return self.type == op.type and self.length == op.length and close(self.score, op.score, 0.0001)