Cython view API: added NUC_SEQS views and sequence classes + changed

cloning API
This commit is contained in:
Celine Mercier
2017-04-21 12:08:14 +02:00
parent 71b1a43df8
commit c2af955b78
5 changed files with 208 additions and 40 deletions

View File

@ -0,0 +1,126 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN
cdef class Seq(dict) :
def __init__(self, str id, object seq, object definition=None) :
self.id = id
self.seq = seq
if definition is not None :
self.definition = definition
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment
return self._id
@id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self._id = new_id
self[bytes2str(ID_COLUMN)] = new_id
# sequence property getter and setter
@property
def seq(self):
return self._seq
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq
self["SEQ"] = new_seq # TODO discuss
# sequence definition property getter and setter
@property
def definition(self):
return self._definition
@definition.setter
def definition(self, object new_definition): # @DuplicatedSignature
self._definition = new_definition
self[bytes2str(DEFINITION_COLUMN)] = new_definition
cdef class Nuc_Seq(Seq) :
# nuc sequence property getter and setter
@property
def seq(self):
return self._seq
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
# sequence quality property getter and setter
@property
def quality(self):
return self._quality
@quality.setter
def quality(self, object new_quality): # @DuplicatedSignature
self._quality = new_quality
self[bytes2str(QUALITY_COLUMN)] = new_quality
# cpdef str reverse_complement(self) : TODO in C ?
# pass
cdef class Nuc_Seq_Stored(Line) :
# TODO store the str version of column name macros?
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment @DuplicatedSignature
return self[bytes2str(ID_COLUMN)]
@id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self[bytes2str(ID_COLUMN)] = new_id
# sequence definition property getter and setter
@property
def definition(self):
return self[bytes2str(DEFINITION_COLUMN)]
@definition.setter
def definition(self, str new_def): # @DuplicatedSignature
self[bytes2str(DEFINITION_COLUMN)] = new_def
# nuc_seq property getter and setter
@property
def nuc_seq(self):
return self[bytes2str(NUC_SEQUENCE_COLUMN)]
@nuc_seq.setter
def nuc_seq(self, object new_seq): # @DuplicatedSignature
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
# quality property getter and setter
@property
def quality(self):
return self[bytes2str(QUALITY_COLUMN)]
@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[bytes2str(QUALITY_COLUMN)] = new_qual
else : # Quality is in str form
(((self._view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self._index, new_qual)
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
return ((self._view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self._index)
# cpdef str reverse_complement(self) : TODO in C ?
# pass
# TODO static method to import OBI_Nuc_Seq to OBI_Nuc_Seq_Stored ?