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Better *Seq* classes but still need work

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This commit is contained in:
Celine Mercier
2017-07-05 17:53:46 +02:00
parent 535fc2af83
commit 313508cc94
1 changed files with 23 additions and 19 deletions
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42
python/obitools3/dms/obiseq.pyx
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@ -3,9 +3,15 @@
from obitools3.utils cimport bytes2str, str2bytes from obitools3.utils cimport bytes2str, str2bytes
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \ ID_COLUMN, \
DEFINITION_COLUMN, \ DEFINITION_COLUMN, \
QUALITY_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)
cdef class Seq(dict) : cdef class Seq(dict) :
@ -23,7 +29,7 @@ cdef class Seq(dict) :
@id.setter @id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self._id = new_id self._id = new_id
self[bytes2str(ID_COLUMN)] = new_id self[ID_COLUMN] = new_id
# sequence property getter and setter # sequence property getter and setter
@property @property
@ -43,7 +49,7 @@ cdef class Seq(dict) :
@definition.setter @definition.setter
def definition(self, object new_definition): # @DuplicatedSignature def definition(self, object new_definition): # @DuplicatedSignature
self._definition = new_definition self._definition = new_definition
self[bytes2str(DEFINITION_COLUMN)] = new_definition self[DEFINITION_COLUMN_str] = new_definition
cdef class Nuc_Seq(Seq) : cdef class Nuc_Seq(Seq) :
@ -56,7 +62,7 @@ cdef class Nuc_Seq(Seq) :
@seq.setter @seq.setter
def seq(self, object new_seq): # @DuplicatedSignature def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq self._seq = new_seq
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq self[NUC_SEQUENCE_COLUMN_str] = new_seq
# sequence quality property getter and setter # sequence quality property getter and setter
@property @property
@ -66,7 +72,7 @@ cdef class Nuc_Seq(Seq) :
@quality.setter @quality.setter
def quality(self, object new_quality): # @DuplicatedSignature def quality(self, object new_quality): # @DuplicatedSignature
self._quality = new_quality self._quality = new_quality
self[bytes2str(QUALITY_COLUMN)] = new_quality self[QUALITY_COLUMN_str] = new_quality
# cpdef str reverse_complement(self) : TODO in C ? # cpdef str reverse_complement(self) : TODO in C ?
# pass # pass
@ -74,49 +80,47 @@ cdef class Nuc_Seq(Seq) :
cdef class Nuc_Seq_Stored(Line) : cdef class Nuc_Seq_Stored(Line) :
# TODO store the str version of column name macros?
# sequence id property getter and setter # sequence id property getter and setter
@property @property
def id(self): # @ReservedAssignment @DuplicatedSignature def id(self): # @ReservedAssignment @DuplicatedSignature
return self[bytes2str(ID_COLUMN)] return self[ID_COLUMN_str]
@id.setter @id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self[bytes2str(ID_COLUMN)] = new_id self[ID_COLUMN_str] = new_id
# sequence definition property getter and setter # sequence definition property getter and setter
@property @property
def definition(self): def definition(self):
return self[bytes2str(DEFINITION_COLUMN)] return self[DEFINITION_COLUMN_str]
@definition.setter @definition.setter
def definition(self, str new_def): # @DuplicatedSignature def definition(self, str new_def): # @DuplicatedSignature
self[bytes2str(DEFINITION_COLUMN)] = new_def self[DEFINITION_COLUMN_str] = new_def
# nuc_seq property getter and setter # nuc_seq property getter and setter
@property @property
def nuc_seq(self): def nuc_seq(self):
return self[bytes2str(NUC_SEQUENCE_COLUMN)] return self[NUC_SEQUENCE_COLUMN_str]
@nuc_seq.setter @nuc_seq.setter
def nuc_seq(self, object new_seq): # @DuplicatedSignature def nuc_seq(self, object new_seq): # @DuplicatedSignature
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq self[NUC_SEQUENCE_COLUMN_str] = new_seq
# quality property getter and setter # quality property getter and setter
@property @property
def quality(self): def quality(self):
return self[bytes2str(QUALITY_COLUMN)] return self[QUALITY_COLUMN_str]
@quality.setter @quality.setter
def quality(self, object new_qual): # @DuplicatedSignature def quality(self, object new_qual): # @DuplicatedSignature
if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
self[bytes2str(QUALITY_COLUMN)] = new_qual self[QUALITY_COLUMN_str] = new_qual
else : # Quality is in str form else : # Quality is in str form
(((self._view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self._index, new_qual) self._view.get_column(QUALITY_COLUMN_str).set_str_line(self._index, new_qual)
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties 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) return self._view.get_column(QUALITY_COLUMN_str).get_str_line(self._index)
# cpdef str reverse_complement(self) : TODO in C ? # cpdef str reverse_complement(self) : TODO in C ?
# pass # pass