Joel L Duerksen

Add streaming support for .gz and .bz2 format input / output files

7

I'm finding very large turtle/triple datasets may be best kept in compressed form, if only to not be throttled by disk I/O max speeds while reading/writing them with a blazing...

.obo SyntaxErorrs

3

What is the best way to force pronto to continue in the face of messy/real data? ``` >>> cl = Ontology("http://purl.obolibrary.org/obo/uberon.obo") Traceback (most recent call last): File "", line 1,...

make[1]: *** No rule to make target 'turtle_lexer.c', needed by 'all'. Stop.

1

Ubuntu 20.04 checked that all listed dependencies installed followed instructions to build from source no errors seen, until the make step ``` make >output.txt ar: `u' modifier ignored since `D'...

pubtator bioc json error - fix bioc json reader? or add new format "pubtator bioc json"?

8

I'm attempting to use bconv to convert BioC JSON to pubtator/TXT, but it throws an error (on validate spanning?). At a glance format appears compliant, but maybe we need a...