Mercurial > repos > earlhaminst > ete

diff ete_species_tree_generator.py @ 15:1e85af7a29c4 draft

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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 e4d5d9a69c9d
line wrap: on
line diff
--- a/ete_species_tree_generator.py	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_species_tree_generator.py	Mon Feb 24 16:34:12 2025 +0000
@@ -18,10 +18,11 @@
 if options.input_species_filename is None:
     parser.error("-s option must be specified, Species list in text format one species in each line")
 
-ncbi = NCBITaxa(dbfile=options.database)
+ncbi = NCBITaxa(dbfile=options.database, update=False)
 with open(options.input_species_filename) as f:
     species_name = [_.strip().replace('_', ' ') for _ in f.readlines()]
 
+breakpoint()
 name2taxid = ncbi.get_name_translator(species_name)
 
 taxid = [name2taxid[_][0] for _ in species_name]