diff --git a/python/obitools3/dms/taxo/taxo.pyx b/python/obitools3/dms/taxo/taxo.pyx index c0f1781..9368094 100755 --- a/python/obitools3/dms/taxo/taxo.pyx +++ b/python/obitools3/dms/taxo/taxo.pyx @@ -1,5 +1,7 @@ #cython: language_level=3 +import sys + from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr from ..capi.obidms cimport OBIDMS_p, obi_dms_get_full_path @@ -34,7 +36,7 @@ cdef class Taxonomy(OBIWrapper) : return (self._pointer) cdef fill_name_dict(self): - print("Indexing taxon names...") + print("Indexing taxon names...", file=sys.stderr) cdef OBIDMS_taxonomy_p pointer = self.pointer() cdef ecotx_t* taxon_p @@ -146,7 +148,9 @@ cdef class Taxonomy(OBIWrapper) : taxo._ranks = [] for r in range((pointer).ranks.count) : taxo._ranks.append(obi_taxo_rank_index_to_label(r, (pointer).ranks)) - + + print('Read %d taxa' % len(taxo), file=sys.stderr) + return taxo @@ -304,6 +308,11 @@ cdef class Taxonomy(OBIWrapper) : def name(self): return self._name + # ranks property getter + @property + def ranks(self): + return self._ranks + def parental_tree_iterator(self, int taxid): """ diff --git a/src/obidms_taxonomy.c b/src/obidms_taxonomy.c index 7bc18e2..e5c8ab6 100755 --- a/src/obidms_taxonomy.c +++ b/src/obidms_taxonomy.c @@ -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->max_taxid = 0; - printf("Reading %d taxa...\n", count_taxa); + fprintf(stderr, "Reading %d taxa...\n", count_taxa); for (i=0; itaxon[i])); @@ -886,9 +886,9 @@ static ecotxidx_t* read_taxonomy_idx(const char* taxa_file_name, const char* loc } 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 - printf("No local taxa\n"); + fprintf(stderr, "No local taxa\n"); count_taxa = taxa_index->count;