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Multiple taxids for a single sequence #54

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nawrockie opened this issue Jan 27, 2021 · 0 comments
Open

Multiple taxids for a single sequence #54

nawrockie opened this issue Jan 27, 2021 · 0 comments

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@nawrockie
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nawrockie commented Jan 27, 2021 •
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@nancyontiveros encountered a failure when running rfci.pl to check in RF00050 which has sequence AE017333.1 in its seed. AE017333.1 has multiple taxids in GenBank (https://www.ncbi.nlm.nih.gov/nuccore/AE017333.1/) due to the presence of prophage sequences in the genome (search for 'taxon' on that page).

Excerpts from the rfci.pl error, reported by Nancy:

A repository hook failed: Commit failed (details follow):: Commit blocked by pre-commit hook

genbank_fetch_seq_info for AE017333.1, > 1 taxids read: 279010 and 1230651

I remember coding this and putting in the check that only 1 taxid be returned per sequence because otherwise we'd have to know which one was correct and it was not immediately obvious how to know that. I'll look into it more now.
nawrockie added a commit that referenced this issue Jan 29, 2021
@nawrockie
Removes requirement that each accession only have 1 taxid from GenBan…
fc33648 
…k, now we take first taxid parsed from GenBank xml; this is github issue #54
@nawrockie nawrockie mentioned this issue Jan 29, 2021
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