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MRG: modify annotate
for flexibility
#2518
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ctb
approved these changes
Mar 9, 2023
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nice and clean! LGTM!
Co-authored-by: C. Titus Brown <titus@idyll.org>
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tax annotate
does not need to require thegather
columns that are required fortax metagenome
andtax genome
.These got especially strict after the recent taxonomy refactor.
This PR modifies
tax annotate
so that it is just looking for a column it can match totaxonomy
assignments. This will allow annotation ofsearch
,prefetch
files and any other file with a good column name.(new) Acceptable column names, in the order
annotate
will look for them:name
(insearch
,gather
output)match_name
(inprefetch
output)ident
accession
Are there any others we should add? We could also let the user specify a column name via cli input, but I don't see the need to enable it unless requested?
Closes #2472