Searched refs:tax2name (Results 1 – 5 of 5) sorted by relevance
| /dports/biology/py-ete3/ete3-3.1.2/ete3/ncbi_taxonomy/ |
| H A D | ncbiquery.py | 490 def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax2rank=None): argument
517 if not tax2name or taxids - set(map(int, list(tax2name.keys()))):
518 tax2name = self.get_taxid_translator(taxids)
523 extra_tax2name = self.get_taxid_translator(list(all_taxid_codes - set(tax2name.keys())))
524 tax2name.update(extra_tax2name)
526 tax2common_name = self.get_common_names(tax2name.keys())
529 tax2rank = self.get_rank(list(tax2name.keys()))
543 n.add_features(sci_name = tax2name.get(node_taxid, getattr(n, taxid_attr, '')),
557 n.add_features(sci_name = tax2name.get(ancestor, str(ancestor)),
562 named_lineage = [tax2name.get(tax, str(tax)) for tax in lineage])
[all …]
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| /dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/ |
| H A D | visualize.py | 212 tax2name = ncbi.get_taxid_translator([taxid])
213 if int(taxid) not in tax2name:
214 print('name', name, taxid, tax2name)
215 return tax2name.get(int(taxid), taxid)
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| /dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/workflow/ |
| H A D | supermatrix.py | 228 tax2name, tax2track = ncbi.annotate_tree_with_taxa(tcopy, None)
231 …broken_branches, broken_clades, broken_clade_sizes, tax2name = ncbi.get_broken_branches(tcopy, n2c…
233 colorify(', '.join(["%s"%tax2name[x] for x in broken_clades]), "wr"))
237 print(["%s"%tax2name[x] for x in broken_branches[branch]])
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| /dports/biology/py-ete3/ete3-3.1.2/ete3/phylo/ |
| H A D | phylotree.py | 746 …def annotate_ncbi_taxa(self, taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, d… argument
798 …return ncbi.annotate_tree(self, taxid_attr=taxid_attr, tax2name=tax2name, tax2track=tax2track, tax…
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| /dports/biology/py-ete3/ete3-3.1.2/ete3/phylomedb/ |
| H A D | phylomeDB3.py | 84 " seed species: %s\n" %(self.tax2name[self.seed_taxid]) +\
120 self.tax2name = {}
124 self.tax2name[taxid] = name
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