def getInsertionSequences(self, fasta, nucleotides = ["C","G","A","T"], up = 10, down = 10):
"""Get sequence content at insertions"""
mat = np.zeros((len(nucleotides), up + down +1))
if np.sum(self.vals) == 0:
return mat
offset = max(up,down)
seq_chunk = Chunk(self.chrom, self.start - offset, self.end + offset)
sequence = get_sequence(seq_chunk, fasta)
seq_mat = seq_to_mat(sequence, nucleotides)
for i in range(self.length()):
mat += self.vals[i] * seq_mat[:,(offset + i - up):(offset + i + down + 1)]
return mat
def getStrandedInsertionSequences(self, fasta, nucleotides = ["C","G","A","T"], up = 10, down = 10):
"""Get sequence content at insertions, taking into account strand"""
mat = np.zeros((len(nucleotides), up + down +1))
if np.sum(self.vals) == 0:
return mat
offset = max(up,down)
seq_chunk = Chunk(self.chrom, self.start - offset, self.end + offset)
sequence = get_sequence(seq_chunk, fasta)
minus_sequence = complement(sequence)
seq_mat = seq_to_mat(sequence, nucleotides)
minus_seq_mat = seq_to_mat(minus_sequence, nucleotides)
for i in range(self.length()):
mat += self.plus[i] * seq_mat[:,(offset + i - up):(offset + i + down + 1)]
mat += self.minus[i] * np.fliplr(minus_seq_mat[:,(offset + i - down):(offset + i + up + 1)])
return mat
