Closed rpetit3 closed 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.
By "all you fixes", do you mean adding single-end and ont support?
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.
Going to close this in favor of https://github.com/CFSAN-Biostatistics/shigatyper/pull/9
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 fastaWith
heparinase
in reference fasta