If you try to use emapper2gbk with the new go-basic.obo file there is an error with pronto. Pronto will return the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/dist-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/usr/local/lib/python3.6/dist-packages/pronto/parsers/obo.py", line 45, in parse_from
raise SyntaxError(s.args[0], location) from None
File "http://purl.obolibrary.org/obo/go/snapshot/go.obo", line 436334
def: "Catalysis of the reaction: behenoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxotetracosanoyl-CoA. + carbon dioxide + coenzyme A." [GOC:pz, Rhea: 36507]␊
^
SyntaxError: expected QuotedString
This is linked to an issue in the current go-basic.obo file (format-version: 1.2, data-version: releases/2021-06-16) due to the space in Rhea: 36507. The issue has been fixed in https://github.com/geneontology/go-ontology/commit/104252cc533a83248ed4df2caefd434e6eb8b531. Before the fix is released in the new version of go-basic.obo you can either download the current go-basic.obo (which can be downloaded at this address: http://purl.obolibrary.org/obo/go/go-basic.obo) and manually corrects the Rhea ID (which is associated to the GO Term GO:0102338). Or you can use an old version of go-basic.obo like the one in the test folder of emapper2gbk.
Description
If you try to use emapper2gbk with the new
go-basic.obo
file there is an error with pronto. Pronto will return the following error:This is linked to an issue in the current go-basic.obo file (
format-version: 1.2, data-version: releases/2021-06-16
) due to the space inRhea: 36507
. The issue has been fixed in https://github.com/geneontology/go-ontology/commit/104252cc533a83248ed4df2caefd434e6eb8b531. Before the fix is released in the new version ofgo-basic.obo
you can either download the currentgo-basic.obo
(which can be downloaded at this address: http://purl.obolibrary.org/obo/go/go-basic.obo) and manually corrects the Rhea ID (which is associated to the GO Term GO:0102338). Or you can use an old version ofgo-basic.obo
like the one in the test folder of emapper2gbk.