Error while converting obo file to owl

[hrshdhgd]

I am trying to convert an obo file (ncbigene.obo) into owl format. This obo file was obtained via pyobo. Code for pyobo is irrelevant here but for the sake of reproducibility:

    from pyobo.sources.ncbigene import get_obo
    obo_file = get_obo()
    obo_file.write_obo(output_path, use_tqdm=True)

When I run the following:

    obo_doc = fastobo.load(input)
    if "default-namespace" not in obo_doc.header:
        obo_doc.header.insert(99, fastobo.header.DefaultNamespaceClause("NCBIGene"))
    if output_format == "owl":
        fastobo.dump_owl(obo_doc, output_path, format="ofn")

I get :

Traceback (most recent call last):
  ...
.../cli.py", line 100, in convert
    obo_doc = fastobo.load(input)
  File "<stdin>", line 203348962
    def: "\\Probable U2 small nuclear ribonucleoprotein B\\\\\\" []
         ^
SyntaxError: expected QuotedString

Would it be possible for fastobo to handle strings like these?

[hrshdhgd]

For now this resolves it:

sed 's/def: "\\\\\(.*\)\\\\\\\\\\\\" \[\]/def: "\1" []/'  source_file.obo > new_file.obo

It was the only artifact so does not make sense for fastobo to do anything.

[althonos]

Reopening this because this is an issue with the grammar, this syntax should be valid (even though the excessive amount of backslashes suggests some sort of export error).

[hrshdhgd]

Thank you!