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comparison ete_species_tree_generator.py @ 15:1e85af7a29c4 draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 16:34:12 +0000
parents 03c10736e497
children
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14:d40b9a7debe5 15:1e85af7a29c4
16 default='no', help='To be used in TreeBest') 16 default='no', help='To be used in TreeBest')
17 options, args = parser.parse_args() 17 options, args = parser.parse_args()
18 if options.input_species_filename is None: 18 if options.input_species_filename is None:
19 parser.error("-s option must be specified, Species list in text format one species in each line") 19 parser.error("-s option must be specified, Species list in text format one species in each line")
20 20
21 ncbi = NCBITaxa(dbfile=options.database) 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()
25 name2taxid = ncbi.get_name_translator(species_name) 26 name2taxid = ncbi.get_name_translator(species_name)
26 27
27 taxid = [name2taxid[_][0] for _ in species_name] 28 taxid = [name2taxid[_][0] for _ in species_name]
28 29
29 tree = ncbi.get_topology(taxid) 30 tree = ncbi.get_topology(taxid)