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