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Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a

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taxonomy C structure
This commit is contained in:
Celine Mercier
2016-10-14 17:03:10 +02:00
parent 0dfd67ec89
commit b63d0fb9fb
7 changed files with 516 additions and 44 deletions
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3
python/obitools3/obidms/_obitaxo.pxd
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@ -1,14 +1,17 @@
#cython: language_level=3
from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from ._obidms cimport OBIDMS
cdef class OBI_Taxonomy :
cdef str _name
cdef OBIDMS_taxonomy_p _pointer
cdef OBIDMS _dms
cpdef close(self)
cpdef _write(self, str prefix)
cdef class OBI_Taxon :

21
python/obitools3/obidms/_obitaxo.pyx
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@ -4,7 +4,10 @@ from obitools3.utils cimport bytes2str, str2bytes
from .capi.obitaxonomy cimport obi_read_taxonomy, \
obi_close_taxonomy, \
obi_taxo_get_taxon_with_taxid
obi_taxo_get_taxon_with_taxid, \
write_rankidx, \
write_taxonomyidx, \
write_nameidx
from ._obidms cimport OBIDMS
@ -18,6 +21,7 @@ cdef class OBI_Taxonomy :
def __init__(self, OBIDMS dms, str name) :
self._dms = dms
self._name = name
self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True) # TODO discuss
# TODO if not found in DMS, try to import?
@ -39,7 +43,16 @@ cdef class OBI_Taxonomy :
cpdef close(self) :
if (obi_close_taxonomy(self._pointer) < 0) :
raise Exception("Error closing the taxonomy")
cpdef _write(self, str prefix) :
if (write_rankidx(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0) :
raise Exception("Error writing the taxonomy rank file")
if (write_taxonomyidx(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0) :
raise Exception("Error writing the taxonomy taxa file")
if (write_nameidx(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0) :
raise Exception("Error writing the taxonomy taxa file")
cdef class OBI_Taxon : # TODO dict subclass?
@ -82,6 +95,6 @@ cdef class OBI_Taxon : # TODO dict subclass?
d['parent'] = self.parent.taxid
d['farest'] = self.farest
return str(d)

4
python/obitools3/obidms/capi/obitaxonomy.pxd
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@ -40,3 +40,7 @@ cdef extern from "obidms_taxonomy.h" nogil:
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
int write_rankidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p taxonomy_name)
int write_taxonomyidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p taxonomy_name)
int write_nameidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p taxonomy_name)