Drew T. Doering

icon indicating a website link https://smc.jgi.doe.gov/

icon company Joint Genome Institute icon location Madison, WI icon location Data Scientist at @JGI-Bioinformatics, working in the Secondary Metabolites Science Program

Results 4 issues of Drew T. Doering

create_db() does not parse directives from GFF files starting in v0.11.0

3 comment

I am trying to read in a GFF that doesn't adhere to spec so I can use `gffutils` to fix it and then write out a corrected file. I've gotten...

needs-discussion

What is the "reserved meaning" of an ampersand (&) in column 9?

From the spec (emphasis mine): > In addition, the following characters have reserved meanings in column 9 and must be escaped when used in other contexts: > > ; semicolon...

Add an `--include all` option to `datasets download genome`

2 comment

**Is your feature request related to a problem? Please describe.** In my workflow, I frequently want to get the latest genome/annotation files for a number of RefSeq (`GCF_*`) and GenBank...

enhancement

Correct link to Bedtools tutorial in the docs

The [main Bedtools docs page](https://bedtools.readthedocs.io/en/latest/index.html) uses an incorrect link to the tutorial, which ends in a 404, so this PR corrects the link to the correct one.