39 lines
1.1 KiB
Cython
Executable File
39 lines
1.1 KiB
Cython
Executable File
#cython: language_level=3
|
|
|
|
from .view.view cimport Line
|
|
|
|
|
|
cdef class Seq(dict) :
|
|
|
|
cpdef object clone(self)
|
|
cpdef str get_str(self)
|
|
cpdef get_symbol_at(self, int pos)
|
|
cpdef get_slice(self, slice slice_to_get)
|
|
|
|
|
|
cdef class Nuc_Seq(Seq) :
|
|
|
|
cdef Nuc_Seq _reverse_complement
|
|
cdef object _quality_array
|
|
cdef bint _revcomp
|
|
cpdef set_quality(self, object new_quality, int offset=*)
|
|
cpdef object build_quality_array(self, list quality)
|
|
cpdef bytes build_reverse_complement(self)
|
|
|
|
|
|
cdef class Seq_Stored(Line) :
|
|
cpdef get_symbol_at(self, int pos)
|
|
cpdef get_slice(self, slice slice_to_get)
|
|
|
|
|
|
cdef class Nuc_Seq_Stored(Seq_Stored) :
|
|
|
|
cdef Nuc_Seq _reverse_complement
|
|
cdef object _quality_array
|
|
cdef bytes _seq
|
|
cpdef set(self, object id, object seq, object definition=*, object quality=*, int offset=*, object tags=*)
|
|
cpdef set_quality_int(self, list new_qual)
|
|
cpdef set_quality_char(self, object new_qual, int offset=*)
|
|
cpdef object build_quality_array(self, list quality)
|
|
cpdef bytes build_reverse_complement(self)
|
|
cpdef str get_str(self) |