Improved taxonomy reading information display

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

View File

@ -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 <OBIDMS_taxonomy_p>(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((<OBIDMS_taxonomy_p>pointer).ranks.count) :
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
@ -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):
"""