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Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to

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be more explicit
This commit is contained in:
Celine Mercier
2019-02-06 18:09:11 +01:00
parent 0b62619e4e
commit 8f18907566
2 changed files with 10 additions and 10 deletions
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2
python/obitools3/dms/obiseq.pxd
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@ -15,7 +15,7 @@ cdef class Nuc_Seq(Seq) :
cdef Nuc_Seq _reverse_complement cdef Nuc_Seq _reverse_complement
cdef object _quality_array cdef object _quality_array
cdef bint _revcomp cdef bint _is_revcomp
cpdef set_quality(self, object new_quality, int offset=*) cpdef set_quality(self, object new_quality, int offset=*)
cpdef object build_quality_array(self, list quality) cpdef object build_quality_array(self, list quality)
cpdef bytes build_reverse_complement(self) cpdef bytes build_reverse_complement(self)

18
python/obitools3/dms/obiseq.pyx
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@ -144,7 +144,7 @@ cdef class Nuc_Seq(Seq) :
if quality is not None: if quality is not None:
self.set_quality(quality, offset=offset) self.set_quality(quality, offset=offset)
self._revcomp = False self._is_revcomp = False
if tags is not None: if tags is not None:
for k in tags: for k in tags:
@ -162,14 +162,14 @@ cdef class Nuc_Seq(Seq) :
new_seq = Nuc_Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone) new_seq = Nuc_Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
return new_seq return new_seq
# revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence) # is_revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence)
@property @property
def revcomp(self): def is_revcomp(self):
return self._revcomp return self._is_revcomp
@revcomp.setter @is_revcomp.setter
def revcomp(self, bint revcomp): # @DuplicatedSignature def is_revcomp(self, bint is_revcomp): # @DuplicatedSignature
self._revcomp = revcomp self._is_revcomp = is_revcomp
# nuc sequence property getter and setter # nuc sequence property getter and setter
@property @property
@ -227,7 +227,7 @@ cdef class Nuc_Seq(Seq) :
else: else:
reversed_quality = None reversed_quality = None
seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self) seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
seq.revcomp = True seq.is_revcomp = True
self._reverse_complement = seq self._reverse_complement = seq
return self._reverse_complement return self._reverse_complement
@ -400,7 +400,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
else: else:
reversed_quality = None reversed_quality = None
seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self) seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
seq.revcomp = True seq.is_revcomp = True
self._reverse_complement = seq self._reverse_complement = seq
return self._reverse_complement return self._reverse_complement