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Improved taxonomy reading information display

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This commit is contained in:
mercierc
2021-07-21 15:20:44 +12:00
parent 6c1a3aff47
commit 747f3efbb2
2 changed files with 14 additions and 5 deletions
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13
python/obitools3/dms/taxo/taxo.pyx
View File

@ -1,5 +1,7 @@
#cython: language_level=3 #cython: language_level=3
import sys
from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr
from ..capi.obidms cimport OBIDMS_p, obi_dms_get_full_path from ..capi.obidms cimport OBIDMS_p, obi_dms_get_full_path
@ -34,7 +36,7 @@ cdef class Taxonomy(OBIWrapper) :
return <OBIDMS_taxonomy_p>(self._pointer) return <OBIDMS_taxonomy_p>(self._pointer)
cdef fill_name_dict(self): cdef fill_name_dict(self):
print("Indexing taxon names...") print("Indexing taxon names...", file=sys.stderr)
cdef OBIDMS_taxonomy_p pointer = self.pointer() cdef OBIDMS_taxonomy_p pointer = self.pointer()
cdef ecotx_t* taxon_p cdef ecotx_t* taxon_p
@ -146,7 +148,9 @@ cdef class Taxonomy(OBIWrapper) :
taxo._ranks = [] taxo._ranks = []
for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) : for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks)) taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
print('Read %d taxa' % len(taxo), file=sys.stderr)
return taxo return taxo
@ -304,6 +308,11 @@ cdef class Taxonomy(OBIWrapper) :
def name(self): def name(self):
return self._name return self._name
# ranks property getter
@property
def ranks(self):
return self._ranks
def parental_tree_iterator(self, int taxid): def parental_tree_iterator(self, int taxid):
""" """

6
src/obidms_taxonomy.c
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@ -873,7 +873,7 @@ static ecotxidx_t* read_taxonomy_idx(const char* taxa_file_name, const char* loc
taxa_index->buffer_size = taxa_index->count; taxa_index->buffer_size = taxa_index->count;
taxa_index->max_taxid = 0; taxa_index->max_taxid = 0;
printf("Reading %d taxa...\n", count_taxa); fprintf(stderr, "Reading %d taxa...\n", count_taxa);
for (i=0; i<count_taxa; i++) for (i=0; i<count_taxa; i++)
{ {
readnext_ecotaxon(f_taxa, &(taxa_index->taxon[i])); readnext_ecotaxon(f_taxa, &(taxa_index->taxon[i]));
@ -886,9 +886,9 @@ static ecotxidx_t* read_taxonomy_idx(const char* taxa_file_name, const char* loc
} }
if (count_local_taxa > 0) if (count_local_taxa > 0)
printf("Reading %d local taxa...\n", count_local_taxa); fprintf(stderr, "Reading %d local taxa...\n", count_local_taxa);
else else
printf("No local taxa\n"); fprintf(stderr, "No local taxa\n");
count_taxa = taxa_index->count; count_taxa = taxa_index->count;