def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
self.assertRaises( RuntimeError, single.matching_statistics, tree, list() );
builder.detach()
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
result = list( single.matching_statistics( tree, [] ) )
self.assertEqual( result, [] )
result = list( single.matching_statistics( tree, list( "QTTATTATTTAGCQWTTAGFK" ) ) )
self.assertEqual(
result,
[
( 0, ( root, 0 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 2, ( leaf_0, 2 ) ),
( 5, ( leaf_0, 5 ) ),
( 4, ( leaf_1, 5 ) ),
( 3, ( leaf_2, 5 ) ),
( 2, ( leaf_3, 5 ) ),
( 1, ( leaf_4, 5 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
( 4, ( leaf_0, 4 ) ),
( 3, ( leaf_1, 4 ) ),
( 2, ( leaf_2, 4 ) ),
( 1, ( leaf_3, 4 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
]
)
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
self.assertRaises( RuntimeError, single.matching_statistics, tree, list() );
builder.detach()
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
result = list( single.matching_statistics( tree, [] ) )
self.assertEqual( result, [] )
result = list( single.matching_statistics( tree, list( "QTTATTATTTAGCQWTTAGFK" ) ) )
self.assertEqual(
result,
[
( 0, ( root, 0 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 2, ( leaf_0, 2 ) ),
( 5, ( leaf_0, 5 ) ),
( 4, ( leaf_1, 5 ) ),
( 3, ( leaf_2, 5 ) ),
( 2, ( leaf_3, 5 ) ),
( 1, ( leaf_4, 5 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
( 4, ( leaf_0, 4 ) ),
( 3, ( leaf_1, 4 ) ),
( 2, ( leaf_2, 4 ) ),
( 1, ( leaf_3, 4 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
]
)
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
builder.detach()
leaf_indices_below = suffixtree.calculate_leaf_indices( root = tree.root )
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
leaf_5 = root[ "$" ]
self.assertEqual( leaf_indices_below[ leaf_0 ], [ 0 ] )
self.assertEqual( leaf_indices_below[ leaf_1 ], [ 1 ] )
self.assertEqual( leaf_indices_below[ leaf_2 ], [ 2 ] )
self.assertEqual( leaf_indices_below[ leaf_3 ], [ 3 ] )
self.assertEqual( leaf_indices_below[ leaf_4 ], [ 4 ] )
self.assertEqual( leaf_indices_below[ leaf_5 ], [ 5 ] )
self.assertEqual( sorted( leaf_indices_below[ branch_t ] ), [ 0, 1 ] )
self.assertEqual( sorted( leaf_indices_below[ root ] ), list(range( 6)) )
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
builder.detach()
leaf_indices_below = suffixtree.calculate_leaf_indices( root = tree.root )
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
leaf_5 = root[ "$" ]
self.assertEqual( leaf_indices_below[ leaf_0 ], [ 0 ] )
self.assertEqual( leaf_indices_below[ leaf_1 ], [ 1 ] )
self.assertEqual( leaf_indices_below[ leaf_2 ], [ 2 ] )
self.assertEqual( leaf_indices_below[ leaf_3 ], [ 3 ] )
self.assertEqual( leaf_indices_below[ leaf_4 ], [ 4 ] )
self.assertEqual( leaf_indices_below[ leaf_5 ], [ 5 ] )
self.assertEqual( sorted( leaf_indices_below[ branch_t ] ), [ 0, 1 ] )
self.assertEqual( sorted( leaf_indices_below[ root ] ), range( 6 ) )
