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Implemented get_collided_fraction method #11

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Implemented get_collided_fraction method #11

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27 changes: 24 additions & 3 deletions looplib/looptools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,6 @@ def get_n_leafs(idx, children):
for child in children[idx]])



def expand_boundary_positions(boundary_positions, offsets=[0]):
"""
Expand boundary_positions by offsets.
Expand All @@ -182,8 +181,6 @@ def expand_boundary_positions(boundary_positions, offsets=[0]):
return expanded_positions.astype(int)




def FRiP(number_of_sites, lef_positions, boundary_positions):
"""
Calculate the Fraction of Reads in Peaks (FRiP).
Expand All @@ -204,3 +201,27 @@ def FRiP(number_of_sites, lef_positions, boundary_positions):
return np.sum(hist[boundary_positions]) / len(lef_positions)


def get_collided_fraction(loops):
"""
Calculate the fraction of collided loops (i.e., flanked on either side by other loops)

Args:
loops (Nx2 int array) : np.ndarray of loop positions

Returns:
float : fraction of collided loops
"""
num_loops = loops.shape[0]

diff_like = np.abs(loops[None,:]-loops[:,None])
diff_cross = np.abs(loops[None,:]-np.flip(loops, axis=-1)[:,None])

np.fill_diagonal(diff_cross[...,0], 0)
np.fill_diagonal(diff_cross[...,1], 0)

collided_like = np.any(diff_like == 1, axis=(1,2))
collided_cross = np.any(diff_cross == 1, axis=(1,2))

num_collided = np.count_nonzero(collided_like + collided_cross)

return float(num_collided) / float(num_loops)