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Reworked taxonomy Cython API to be a subclass of OBIWrapper

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This commit is contained in:
Celine Mercier
2017-04-21 11:54:05 +02:00
parent ab0d08293e
commit 1725b8b80c
3 changed files with 96 additions and 32 deletions
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0
python/obitools3/dms/taxo/__init__.py Normal file
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12
python/obitools3/dms/taxo/taxo.pxd
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@ -4,12 +4,16 @@ from ..capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from ..dms cimport DMS
from ..object cimport OBIWrapper
cdef class OBI_Taxonomy :
cdef str _name
cdef OBIDMS_taxonomy_p _pointer
cdef OBIDMS _dms
cdef class OBI_Taxonomy(OBIWrapper) :
cdef str _name # TODO keep as bytes?
cdef DMS _dms
cdef inline OBIDMS_taxonomy_p pointer(self)
cpdef get_taxon_by_idx(self, int idx)
cpdef write(self, str prefix)
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*)
cpdef close(self)

88
python/obitools3/dms/taxo/taxo.pyx
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@ -14,18 +14,38 @@ from ..capi.obitaxonomy cimport obi_read_taxonomy, \
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
cdef class OBI_Taxonomy :
cdef class OBI_Taxonomy(OBIWrapper) :
# TODO function to import taxonomy?
def __init__(self, OBIDMS dms, str name, bint taxdump=False) :
self._dms = dms
self._name = name
cdef inline OBIDMS_taxonomy_p pointer(self) :
return <OBIDMS_taxonomy_p>(self._pointer)
@staticmethod
def open(DMS dms, str name, bint taxdump=False) :
cdef void* pointer
cdef OBI_Taxonomy taxo
if taxdump :
self._pointer = obi_read_taxdump(tobytes(name))
pointer = <void*>obi_read_taxdump(tobytes(name))
else :
self._pointer = obi_read_taxonomy(dms._pointer, tobytes(name), True) # TODO discuss
pointer = <void*>obi_read_taxonomy(dms.pointer(), tobytes(name), True) # TODO discuss
# TODO if not found in DMS, try to import?
if pointer == NULL :
raise RuntimeError("Error : Cannot read taxonomy %s"
% name)
taxo = OBIWrapper.new(OBI_Taxonomy, pointer)
dms.register(taxo)
taxo._dms = dms
taxo._name = name
return taxo
def __getitem__(self, object ref):
@ -33,7 +53,7 @@ cdef class OBI_Taxonomy :
cdef object taxon_capsule
if type(ref) == int :
taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref)
taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer(), ref)
if taxon_p == NULL :
raise Exception("Taxon not found")
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
@ -42,6 +62,22 @@ cdef class OBI_Taxonomy :
raise Exception("Not implemented")
cpdef get_taxon_by_idx(self, int idx):
cdef ecotx_t* taxa
cdef ecotx_t* taxon_p
cdef object taxon_capsule
taxa = self.pointer().taxa.taxon
taxon_p = <ecotx_t*> (taxa+idx)
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
return OBI_Taxon(taxon_capsule, self)
def __len__(self):
return self.pointer().taxa.count
def __iter__(self):
cdef ecotx_t* taxa
@ -49,23 +85,23 @@ cdef class OBI_Taxonomy :
cdef object taxon_capsule
cdef int t
taxa = self._pointer.taxa.taxon
taxa = self.pointer().taxa.taxon
# Yield each taxid
for t in range(self._pointer.taxa.count):
for t in range(self.pointer().taxa.count):
taxon_p = <ecotx_t*> (taxa+t)
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
yield OBI_Taxon(taxon_capsule, self)
cpdef write(self, str prefix) :
if obi_write_taxonomy(self._dms._pointer, self._pointer, tobytes(prefix)) < 0 :
if obi_write_taxonomy(self._dms.pointer(), self.pointer(), tobytes(prefix)) < 0 :
raise Exception("Error writing the taxonomy to binary files")
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) :
cdef int taxid
taxid = obi_taxo_add_local_taxon(self._pointer, tobytes(name), tobytes(rank_name), parent_taxid, min_taxid)
taxid = obi_taxo_add_local_taxon(self.pointer(), tobytes(name), tobytes(rank_name), parent_taxid, min_taxid)
if taxid < 0 :
raise Exception("Error adding a new taxon to the taxonomy")
else :
@ -73,8 +109,21 @@ cdef class OBI_Taxonomy :
cpdef close(self) :
if (obi_close_taxonomy(self._pointer) < 0) :
raise Exception("Error closing the taxonomy")
cdef OBIDMS_taxonomy_p pointer = self.pointer()
if self.active() :
self._dms.unregister(self)
OBIWrapper.close(self)
if (obi_close_taxonomy(self.pointer()) < 0) :
raise Exception("Problem closing the taxonomy %s" %
self._name)
# name property getter
@property
def name(self):
return self._name
cdef class OBI_Taxon : # TODO dict subclass?
@ -86,6 +135,16 @@ cdef class OBI_Taxon : # TODO dict subclass?
self._tax = tax
# To test equality
def __richcmp__(self, OBI_Taxon taxon2, int op):
return (self.name == taxon2.name) and \
(self.taxid == taxon2.taxid) and \
(self.rank == taxon2.rank) and \
(self.farest == taxon2.farest) and \
(self.parent.taxid == taxon2.parent.taxid) and \
(self.preferred_name == taxon2.preferred_name)
# name property getter
@property
def name(self):
@ -121,13 +180,14 @@ cdef class OBI_Taxon : # TODO dict subclass?
@preferred_name.setter
def preferred_name(self, str new_preferred_name) : # @DuplicatedSignature
if (obi_taxo_add_preferred_name_with_taxon(self._tax._pointer, self._pointer, tobytes(new_preferred_name)) < 0) :
if (obi_taxo_add_preferred_name_with_taxon(self._tax.pointer(), self._pointer, tobytes(new_preferred_name)) < 0) :
raise Exception("Error adding a new preferred name to a taxon")
def __repr__(self):
d = {}
d['taxid'] = self.taxid
d['name'] = self.name
d['rank'] = self.rank
d['preferred name'] = self.preferred_name
d['parent'] = self.parent.taxid
d['farest'] = self.farest