d8a257e711
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx, merged.dmp and delnodes.dmp files.
116 lines
3.2 KiB
Cython
116 lines
3.2 KiB
Cython
#cython: language_level=3
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from obitools3.utils cimport bytes2str, str2bytes
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from .capi.obitaxonomy cimport obi_read_taxonomy, \
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obi_read_taxdump, \
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obi_write_taxonomy, \
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obi_close_taxonomy, \
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obi_taxo_get_taxon_with_taxid
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from ._obidms cimport OBIDMS
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from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
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from logging import raiseExceptions
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cdef class OBI_Taxonomy :
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# TODO function to import taxonomy?
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def __init__(self, OBIDMS dms, str name, bint taxdump=False) :
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self._dms = dms
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self._name = name
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if taxdump :
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self._pointer = obi_read_taxdump(str2bytes(name))
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else :
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self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True) # TODO discuss
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# TODO if not found in DMS, try to import?
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def __getitem__(self, object ref):
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cdef ecotx_t* taxon_p
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cdef object taxon_capsule
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if type(ref) == int :
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taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref)
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taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
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return OBI_Taxon(taxon_capsule)
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else :
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raise Exception("Not implemented")
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# def __iter__(self):
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#
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# cdef ecotx_t* taxa
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# cdef ecotx_t* taxon_p
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# cdef object taxon_capsule
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#
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# taxa = self._pointer.taxa.taxon
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#
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# # Yield each taxid
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# for t in range(self._pointer.taxa.count):
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# taxon_p = taxa+t # TODO not compiling for mysterious cython reasons
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# taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
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# yield OBI_Taxon(taxon_capsule)
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cpdef write(self, str prefix) :
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if obi_write_taxonomy(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0 :
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raise Exception("Error writing the taxonomy to binary files")
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cpdef close(self) :
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if (obi_close_taxonomy(self._pointer) < 0) :
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raise Exception("Error closing the taxonomy")
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cdef class OBI_Taxon : # TODO dict subclass?
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def __init__(self, object taxon_capsule) :
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self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
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if self._pointer == NULL :
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raise Exception("Error reading the taxonomy")
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# name property getter
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@property
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def name(self):
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return bytes2str(self._pointer.name)
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# taxid property getter
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@property
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def taxid(self):
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return self._pointer.taxid
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# rank property getter
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@property
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def rank(self):
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return self._pointer.rank
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# farest property getter
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@property
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def farest(self):
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return self._pointer.farest
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# parent property getter
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@property
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def parent(self):
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cdef object parent_capsule
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parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
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return OBI_Taxon(parent_capsule)
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def __repr__(self):
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d = {}
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d['taxid'] = self.taxid
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d['name'] = self.name
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d['parent'] = self.parent.taxid
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d['farest'] = self.farest
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return str(d)
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