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Provide informative error when UPAC code hit and tool fails. #5

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jfy133 opened this issue Apr 20, 2021 · 0 comments
Open

Provide informative error when UPAC code hit and tool fails. #5

jfy133 opened this issue Apr 20, 2021 · 0 comments

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@jfy133
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jfy133 commented Apr 20, 2021

Some of the 'genomes' I downloaded and tried to input were actually unfinished assemblies:

e.g. GCA_001057035.1_ASM105703v1_genomic.fna

These contained symbols such as W/R/S in the sequence itself.

I would suggest that either if this is encountered that adrsm reports a nice error (rather than traceback) stating this isn't accepted, and please fix.

You could also suggest the following command to clean it up:

sed -i '/^[^>]/s/[R|Y|W|S|M|K|H|B|V|D]/N/g' *.fna
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