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Making the --concat_target_taxa argument optional

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Auden Cote-L'Heureux 2025-04-15 16:23:19 -04:00 committed by GitHub
parent 2651fe7b89
commit e452ae0117
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1 changed files with 1 additions and 2 deletions
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PTL2/Scripts/concatenate.py
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@ -126,8 +126,7 @@ def remove_paralogs(params):
elif params.concat_target_taxa != None: elif params.concat_target_taxa != None:
target_codes = [params.concat_target_taxa] target_codes = [params.concat_target_taxa]
else: else:
print('\nERROR: missing --concat_target_taxa argument. When concatenating, you need to give the taxonomic group (sequence prefix), groups, or a file containing a list of groups (multiple prefixes) for which to select sequences to construct a concatenated alignment\n') target_codes = [leaf.name[:10] for leaf in tree]
exit()
monophyletic_clades = { } monophyletic_clades = { }