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Added functions to add new taxa to a taxonomy with handling of

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associated *.ldx files
This commit is contained in:
Celine Mercier
2016-11-03 17:59:21 +01:00
parent 2504bf0fa9
commit 2d2fe5279d
5 changed files with 664 additions and 397 deletions
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3
python/obitools3/obidms/_obitaxo.pxd
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@ -10,8 +10,9 @@ cdef class OBI_Taxonomy :
cdef OBIDMS_taxonomy_p _pointer
cdef OBIDMS _dms
cpdef close(self)
cpdef write(self, str prefix)
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*)
cpdef close(self)
cdef class OBI_Taxon :

14
python/obitools3/obidms/_obitaxo.pyx
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@ -7,6 +7,7 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
obi_write_taxonomy, \
obi_close_taxonomy, \
obi_taxo_get_taxon_with_taxid, \
obi_taxonomy_add_local_taxon, \
ecotx_t
@ -38,6 +39,8 @@ cdef class OBI_Taxonomy :
if type(ref) == int :
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)
return OBI_Taxon(taxon_capsule)
else :
@ -55,7 +58,7 @@ cdef class OBI_Taxonomy :
# Yield each taxid
for t in range(self._pointer.taxa.count):
taxon_p = <ecotx_t*> (taxa+t) # TODO not compiling for mysterious cython reasons
taxon_p = <ecotx_t*> (taxa+t)
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
yield OBI_Taxon(taxon_capsule)
@ -65,6 +68,15 @@ cdef class OBI_Taxonomy :
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_taxonomy_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid)
if taxid < 0 :
raise Exception("Error adding a new taxon to the taxonomy")
else :
return taxid
cpdef close(self) :
if (obi_close_taxonomy(self._pointer) < 0) :
raise Exception("Error closing the taxonomy")

1
python/obitools3/obidms/capi/obitaxonomy.pxd
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@ -56,3 +56,4 @@ cdef extern from "obidms_taxonomy.h" nogil:
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)

1033
src/obidms_taxonomy.c
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File diff suppressed because it is too large Load Diff

10
src/obidms_taxonomy.h
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@ -17,6 +17,10 @@
#include "obidms.h"
#define MIN_LOCAL_TAXID (10000000)
#define TAX_NAME_LEN (1024)
typedef struct {
int32_t taxid;
int32_t rank;
@ -33,11 +37,14 @@ typedef struct ecotxnode {
int32_t idx;
struct ecotxnode* parent;
char* name;
bool local;
} ecotx_t;
typedef struct {
int32_t count;
int32_t ncbi_count;
int32_t local_count;
int32_t max_taxid;
int32_t buffer_size;
ecotx_t taxon[1];
@ -74,6 +81,8 @@ typedef struct {
typedef struct OBIDMS_taxonomy_t {
char tax_name[TAX_NAME_LEN];
OBIDMS_p dms;
ecorankidx_t* ranks;
econameidx_t* names;
ecotxidx_t* taxa;
@ -109,3 +118,4 @@ int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name
OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump);
int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);