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CFSAN-Biostatistics / shigatyper

CFSAN Shigella Typing Pipeline
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add heparinase to reference fasta #8

Closed rpetit3 closed 2 years ago

rpetit3 commented 2 years ago

This is related to https://github.com/CFSAN-Biostatistics/shigatyper/issues/6

Adds the gene sequence for heparinase (https://www.ncbi.nlm.nih.gov/nuccore/CP016036.1?from=2803&to=4428&report=fasta&strand=2) required for calling Shigella boydii serotype 20

Without heparinase in reference fasta

sample  prediction      ipaB
SRX1486859      Shigella boydii serotype 1      -

With heparinase in reference fasta

sample  prediction      ipaB
SRX1486859      Shigella boydii serotype 20     -
florathecat commented 2 years ago

Thanks Robert,

We just realized the missing heparinase gene from the reference fasts file and have not add it back. Can you please merge your loop with all your fixes?

I’ll get to it later with the shigatoxins after I figure out what else are missing.

Thanks,

On Feb 11, 2022, at 1:10 AM, Robert A. Petit III @.***> wrote:

 This is related to #6

Adds the gene sequence for heparinase (https://www.ncbi.nlm.nih.gov/nuccore/CP016036.1?from=2803&to=4428&report=fasta&strand=2) required for calling Shigella boydii serotype 20

Without heparinase in reference fasta

sample prediction ipaB SRX1486859 Shigella boydii serotype 1 - With heparinase in reference fasta

sample prediction ipaB SRX1486859 Shigella boydii serotype 20 - You can view, comment on, or merge this pull request online at:

https://github.com/CFSAN-Biostatistics/shigatyper/pull/8

Commit Summary

19dc7ac add heparinase to reference fasta File Changes (1 file) M shigatyper/resources/ShigellaRef5.fasta (28) Patch Links:

https://github.com/CFSAN-Biostatistics/shigatyper/pull/8.patch https://github.com/CFSAN-Biostatistics/shigatyper/pull/8.diff — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.

rpetit3 commented 2 years ago

By "all you fixes", do you mean adding single-end and ont support?

florathecat commented 2 years ago

Yes please. I guess I wasn’t being explicit. My apologies.

On Feb 11, 2022, at 10:01 AM, Robert A. Petit III @.***> wrote:

 By "all you fixes", do you mean adding single-end and ont support?

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.

rpetit3 commented 2 years ago

Going to close this in favor of https://github.com/CFSAN-Biostatistics/shigatyper/pull/9