def __init__(self, chrom, start, end, name="track", vals=None, log=False):
Chunk.__init__(self, chrom, start, end, name=name)
self.log = log
if vals is None:
self.vals = None
elif len(vals) == self.length():
self.vals = vals
else:
raise Exception("Input vals must be of length as set by start and end!")
def __init__(self, chrom, start, end, name = "track", vals=None , log = False):
Chunk.__init__(self, chrom, start, end, name = name)
self.log = log
if vals is None:
self.vals = None
elif len(vals) == self.length():
self.vals = vals
else:
raise Exception("Input vals must be of length as set by start and end!")
def slop(self, chromDict, up=0, down=0, new=False):
"""Modification of slop method for Chunk class to check if vals are set"""
if self.vals is None:
out = Chunk.slop(self, chromDict, up=up, down=down, new=new)
return out
else:
raise Exception("Cannot slop Track if vals are set")
def slop(self, chromDict, up=0, down=0, new=False):
"""Modification of slop method for Chunk class to check if vals are set"""
if self.vals is None:
out = Chunk.slop(self, chromDict, up=up, down=down, new=new)
return out
else:
raise Exception("Cannot slop Track if vals are set")
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
