Closed serenalotreck closed 2 years ago
Thanks for the terrific contribution.
I added functionality for an issue similar to yours to the obo reader for issue 202 (accepting ontologies like the Human Phenotype Ontology (HPO))
I exposed some annotation file issues exposed upon running the regression tests prior to pushing ( https://github.com/geneontology/helpdesk/issues/358 and https://github.com/geneontology/helpdesk/issues/359)
After I resolve the test issues, I will push the new functionality for issue 202.
Thank you again for your interest in GOA TOOLs, for taking the time to write us, and for the terrific code contribution.
Thanks so much for the quick response & merge!
I'm trying to use
GafReader
to read in GAF files for the Planteome database. These files are GAF 2.0 compliant with one exception -- in the "Aspect" column (NS
in theGafReader.associations
named tuple), there are letters besides theP
,F
, andC
that are specified in the GAF docs.As a result, when I run the tool, I get the following error:
Would it be possible to allow the
NS
field to have any letter? I'm trying to avoid writing my own GAF parser since you already have what seems to be a fairly robust one, but I'm not sure how else to get around this issue.Thanks!