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nhoffman / ya16sdb

A curated subset of 16S rRNA sequences from NCBI
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Best match 16S type strain record in ya16sdb web interface does not match data in NGS16S output #44

Closed marykstewart closed 2 years ago

marykstewart commented 2 years ago

Hi Chris, linking here to the issue I made in the molmicro github a couple of weeks ago https://gitlab.labmed.uw.edu/molmicro/mkrefpkg/-/issues/83

Will this be part of the upcoming release?

It just occurred to me...is this why you and Noah think there is a misclassified E. faecalis type strain, WRT example NZ_CABGZA010000007_337_1876 (coordinates have changed slightly)? It seems like this must just be the ya16sdb web interface bug. There are no Enterococcus type strains in the NCBI_16s_types_details when that 'Enterococcus faecalis' record is blasted...and that database is unfiltered, so if there was one lurking, it should show up. https://share.labmed.uw.edu/molmicro/sanger/report/2021/09/30/2053025_ad_hoc_20210930150544_NZ_CABGZA010000007_337_1876.html

Screen Shot 2021-09-30 at 3 02 09 PM Screen Shot 2021-09-30 at 3 09 46 PM Screen Shot 2021-09-30 at 3 11 39 PM
crosenth commented 2 years ago

Yes that is a bug in the web interface, the nearest type strain is just itself. This bug has been lingering for a while but it should hopefully, finally be fixed with this release

crosenth commented 2 years ago

This should be fixed with the bump in Pandas version in the requirements.txt file https://github.com/nhoffman/ya16sdb/commit/dbf470d311583ce9c768da15b8be6dbdd1824edc