Closed gmhhope closed 2 years ago
@gmhhope thanks for reporting this bug that should be fixed by applying annotateGEM
function to Mouse-GEM before exporting as .xml
.
@gmhhope thanks for reporting this bug that should be fixed by applying
annotateGEM
function to Mouse-GEM before exporting as.xml
.
Dear Haowang,
Thanks for replying me! Could you elaborate on what exactly the function annotateGEM
from and how to apply? And I was trying to read your Mouse-GEM.xml
file instead of exporting it. So I got confused.
Thanks, Minghao Gong
@gmhhope the annoateGEM function is from Human-GEM and usually applied while releasing new version. We'll incorporate this step to Mouse-GEM in future release.
this has been fixed in v1.3
Description of the issue:
Metabolite Identifiers are not in the COBRApy-parsed
Mouse-GEM.xml
. The same scenario are inRat-GEM.xml
,Mouse-GEM
,Rat-GEM
,Worm-GEM
andZebrafish-GEM
(also see https://github.com/SysBioChalmers/Zebrafish-GEM/issues/5). In addition,Fruitfly-GEM
cannot be parsed using COBRApy(see https://github.com/SysBioChalmers/Fruitfly-GEM/issues/5).Expected feature/value/output:
Expect to have identifiers in
.xml
files synchronized with flatfilesmetabolite.tsv
.Current feature/value/output:
In humanGEM, everything is nicely showed up:
But in Mouse-GEM, Worm-GEM ...: Same codes result in:
I hereby confirm that I have:
master
branch of the repository