def __getitem__(self, slice_data):
"""
Interpret slice data and return region of sequence from twobit file
"""
start, stop, stride = slice_data.indices(self.size)
assert stride == 1, "striding in slices not supported"
if stop - start < 1:
return ""
return _twobit.read(self.twobit_file, self, start, stop, False)
def get( self, start, end ):
# Trim start / stop
if start < 0:
start = 0
if end > seq.size:
end = seq.size
out_size = end - start
if out_size < 1:
raise Exception( "end before start (%s,%s)" % ( start,end ) )
# Find position of packed portion
dna = _twobit.read( self.tbf.file, self, start, end, self.tbf.do_mask )
# Return
return dna
def get(self, start, end):
# Trim start / stop
if start < 0:
start = 0
if end > self.size:
end = self.size
out_size = end - start
if out_size < 1:
raise Exception("end before start (%s,%s)" % (start, end))
# Find position of packed portion
dna = _twobit.read(self.tbf.file, self, start, end, self.tbf.do_mask)
# Return
return dna
def get(self, start, end):
"""Get region of sequence from twobit file"""
# Trim start / stop
if start < 0:
start = 0
if end > self.size:
end = self.size
out_size = end - start
if out_size < 1:
raise Exception("end before start (%s, %s)" % (start, end))
# Find position of packed portion
dna = _twobit.read(self.twobit_file, self, start, end, False)
# Return
return dna
def __getitem__( self, slice ):
start, stop, stride = slice.indices( self.size )
assert stride == 1, "Striding in slices not supported"
if stop - start < 1:
return ""
return _twobit.read( self.tbf.file, self, start, stop, self.tbf.do_mask )
def __getitem__(self, slice):
start, stop, stride = slice.indices(self.size)
assert stride == 1, "Striding in slices not supported"
if stop - start < 1:
return ""
return _twobit.read(self.tbf.file, self, start, stop, self.tbf.do_mask)