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comparison ete_species_tree_generator.py @ 16:e4d5d9a69c9d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:28:17 +0000
parents 1e85af7a29c4
children
comparison
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15:1e85af7a29c4 16:e4d5d9a69c9d
20 20
21 ncbi = NCBITaxa(dbfile=options.database, update=False) 21 ncbi = NCBITaxa(dbfile=options.database, update=False)
22 with open(options.input_species_filename) as f: 22 with open(options.input_species_filename) as f:
23 species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] 23 species_name = [_.strip().replace('_', ' ') for _ in f.readlines()]
24 24
25 breakpoint()
26 name2taxid = ncbi.get_name_translator(species_name) 25 name2taxid = ncbi.get_name_translator(species_name)
27 26
28 taxid = [name2taxid[_][0] for _ in species_name] 27 taxid = [name2taxid[_][0] for _ in species_name]
29 28
30 tree = ncbi.get_topology(taxid) 29 tree = ncbi.get_topology(taxid)