Cython API: Seq classes reworked
This commit is contained in:
Celine Mercier
@ -4,10 +4,7 @@ from .view.view cimport Line
|
||||
|
||||
|
||||
cdef class Seq(dict) :
|
||||
|
||||
cdef str _id
|
||||
cdef object _seq
|
||||
cdef str _definition
|
||||
cdef dict _annotations
|
||||
|
||||
|
||||
cdef class Nuc_Seq(Seq) :
|
||||
@ -16,7 +13,12 @@ cdef class Nuc_Seq(Seq) :
|
||||
#cpdef object reverse_complement(self)
|
||||
|
||||
|
||||
cdef class Nuc_Seq_Stored(Line) :
|
||||
cdef class Seq_Stored(Line) :
|
||||
pass
|
||||
|
||||
cpdef object get_str_quality(self)
|
||||
|
||||
cdef class Nuc_Seq_Stored(Seq_Stored) :
|
||||
|
||||
cpdef set_quality_int(self, list new_qual)
|
||||
cpdef set_quality_char(self, bytes new_qual, int offset=*)
|
||||
#cpdef object reverse_complement(self)
|
||||
@ -1,55 +1,68 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.utils cimport bytes2str, str2bytes
|
||||
from obitools3.utils cimport bytes2str, str2bytes, tostr, tobytes
|
||||
|
||||
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
||||
ID_COLUMN, \
|
||||
DEFINITION_COLUMN, \
|
||||
QUALITY_COLUMN
|
||||
|
||||
|
||||
NUC_SEQUENCE_COLUMN_str = bytes2str(NUC_SEQUENCE_COLUMN)
|
||||
ID_COLUMN_str = bytes2str(ID_COLUMN)
|
||||
DEFINITION_COLUMN_str = bytes2str(DEFINITION_COLUMN)
|
||||
QUALITY_COLUMN_str = bytes2str(QUALITY_COLUMN)
|
||||
QUALITY_COLUMN, \
|
||||
COUNT_COLUMN
|
||||
|
||||
|
||||
cdef class Seq(dict) :
|
||||
def __init__(self, str id, object seq, object definition=None) :
|
||||
self.id = id
|
||||
self.seq = seq
|
||||
def __init__(self, object id, object seq, object definition=None, object quality=None, int offset=-1, object tags=None) :
|
||||
cdef object k
|
||||
cdef bytes k_b
|
||||
self[ID_COLUMN] = tobytes(id)
|
||||
self.seq = tobytes(seq)
|
||||
if definition is not None :
|
||||
self.definition = definition
|
||||
self.definition = tobytes(definition)
|
||||
self._annotations = {}
|
||||
if tags is not None :
|
||||
for k in tags:
|
||||
k_b = tobytes(k)
|
||||
self[k_b] = tags[k_b]
|
||||
|
||||
|
||||
def __contains__(self, object key):
|
||||
return dict.__contains__(self, tobytes(key))
|
||||
|
||||
|
||||
# sequence id property getter and setter
|
||||
@property
|
||||
def id(self): # @ReservedAssignment
|
||||
return self._id
|
||||
return self[ID_COLUMN]
|
||||
|
||||
@id.setter
|
||||
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
|
||||
self._id = new_id
|
||||
self[ID_COLUMN] = new_id
|
||||
def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
|
||||
self[ID_COLUMN] = tobytes(new_id)
|
||||
|
||||
# sequence annotations property getter and setter
|
||||
@property
|
||||
def annotations(self): # @ReservedAssignment
|
||||
return self._annotations
|
||||
|
||||
@annotations.setter
|
||||
def annotations(self, object annotations): # @ReservedAssignment @DuplicatedSignature
|
||||
self._annotations = annotations
|
||||
|
||||
# sequence property getter and setter
|
||||
@property
|
||||
def seq(self):
|
||||
return self._seq
|
||||
return self[b"SEQ"]
|
||||
|
||||
@seq.setter
|
||||
def seq(self, object new_seq): # @DuplicatedSignature
|
||||
self._seq = new_seq
|
||||
self["SEQ"] = new_seq # TODO discuss
|
||||
self[b"SEQ"] = tobytes(new_seq)
|
||||
|
||||
# sequence definition property getter and setter
|
||||
@property
|
||||
def definition(self):
|
||||
return self._definition
|
||||
return self[DEFINITION_COLUMN]
|
||||
|
||||
@definition.setter
|
||||
def definition(self, object new_definition): # @DuplicatedSignature
|
||||
self._definition = new_definition
|
||||
self[DEFINITION_COLUMN_str] = new_definition
|
||||
self[DEFINITION_COLUMN] = tobytes(new_definition)
|
||||
|
||||
|
||||
cdef class Nuc_Seq(Seq) :
|
||||
@ -62,65 +75,82 @@ cdef class Nuc_Seq(Seq) :
|
||||
@seq.setter
|
||||
def seq(self, object new_seq): # @DuplicatedSignature
|
||||
self._seq = new_seq
|
||||
self[NUC_SEQUENCE_COLUMN_str] = new_seq
|
||||
self[NUC_SEQUENCE_COLUMN] = tobytes(new_seq)
|
||||
|
||||
# sequence quality property getter and setter
|
||||
@property
|
||||
def quality(self):
|
||||
return self._quality
|
||||
return self[QUALITY_COLUMN]
|
||||
|
||||
@quality.setter
|
||||
def quality(self, object new_quality): # @DuplicatedSignature
|
||||
self._quality = new_quality
|
||||
self[QUALITY_COLUMN_str] = new_quality
|
||||
self[QUALITY_COLUMN] = tobytes(new_quality)
|
||||
|
||||
# cpdef str reverse_complement(self) : TODO in C ?
|
||||
# pass
|
||||
|
||||
|
||||
cdef class Nuc_Seq_Stored(Line) :
|
||||
cdef class Seq_Stored(Line) :
|
||||
|
||||
# sequence id property getter and setter
|
||||
@property
|
||||
def id(self): # @ReservedAssignment @DuplicatedSignature
|
||||
return self[ID_COLUMN_str]
|
||||
return self._view.get_column(ID_COLUMN).get_line(self.index)
|
||||
|
||||
@id.setter
|
||||
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
|
||||
self[ID_COLUMN_str] = new_id
|
||||
def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
|
||||
self._view.get_column(ID_COLUMN).set_line(self._index, tobytes(new_id))
|
||||
|
||||
# sequence definition property getter and setter
|
||||
@property
|
||||
def definition(self):
|
||||
return self[DEFINITION_COLUMN_str]
|
||||
return self._view.get_column(DEFINITION_COLUMN).get_line(self.index)
|
||||
|
||||
@definition.setter
|
||||
def definition(self, str new_def): # @DuplicatedSignature
|
||||
self[DEFINITION_COLUMN_str] = new_def
|
||||
def definition(self, object new_def): # @DuplicatedSignature
|
||||
self._view.get_column(DEFINITION_COLUMN).set_line(self._index, tobytes(new_def))
|
||||
|
||||
|
||||
cdef class Nuc_Seq_Stored(Seq_Stored) :
|
||||
|
||||
cpdef set_quality_int(self, list new_qual):
|
||||
self._view.get_column(QUALITY_COLUMN).set_line(self.index, new_qual)
|
||||
|
||||
cpdef set_quality_char(self, bytes new_qual, int offset=-1):
|
||||
self._view.get_column(QUALITY_COLUMN).set_str_line(self.index, new_qual, offset=offset)
|
||||
|
||||
# nuc_seq property getter and setter
|
||||
@property
|
||||
def nuc_seq(self):
|
||||
return self[NUC_SEQUENCE_COLUMN_str]
|
||||
return self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index)
|
||||
|
||||
@nuc_seq.setter
|
||||
def nuc_seq(self, object new_seq): # @DuplicatedSignature
|
||||
self[NUC_SEQUENCE_COLUMN_str] = new_seq
|
||||
self._view.get_column(NUC_SEQUENCE_COLUMN).set_line(self.index, tobytes(new_seq))
|
||||
|
||||
# quality property getter and setter
|
||||
@property
|
||||
def quality(self):
|
||||
return self[QUALITY_COLUMN_str]
|
||||
return self._view.get_column(QUALITY_COLUMN).get_line(self.index)
|
||||
|
||||
@quality.setter
|
||||
def quality(self, object new_qual): # @DuplicatedSignature
|
||||
if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
|
||||
self[QUALITY_COLUMN_str] = new_qual
|
||||
else : # Quality is in str form
|
||||
self._view.get_column(QUALITY_COLUMN_str).set_str_line(self._index, new_qual)
|
||||
if (new_qual is None) or (type(new_qual) == list) : # TODO check that quality column exists
|
||||
self._view.get_column(QUALITY_COLUMN).set_line(self._index, new_qual)
|
||||
elif (type(new_qual) == str) or (type(new_qual) == bytes) : # Quality is in str form
|
||||
self._view.get_column(QUALITY_COLUMN).set_str_line(self._index, tobytes(new_qual))
|
||||
else :
|
||||
raise Exception("Sequence quality in unrecognized format")
|
||||
|
||||
# quality character string property getter
|
||||
@property
|
||||
def quality_str(self):
|
||||
return self._view.get_column(QUALITY_COLUMN).get_str_line(self._index)
|
||||
|
||||
|
||||
def __str__(self):
|
||||
return bytes2str(self.nuc_seq)
|
||||
|
||||
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
|
||||
return self._view.get_column(QUALITY_COLUMN_str).get_str_line(self._index)
|
||||
|
||||
# cpdef str reverse_complement(self) : TODO in C ?
|
||||
# pass
|
||||
|
||||
Reference in New Issue
Block a user