convert
- convert(input_path: str | Path, output_path: str | Path, input_flag: typing_extensions.Literal[-i, -I] | None = None, *, merge: bool = True, fmt: str | None = None, check: bool = True, reason: bool = False, extra_args: List[str] | None = None) str [source]
Convert an OBO file to an OWL file with ROBOT.
- Parameters:
input_path – Either a local file path or IRI. If a local file path is used, pass
"-i"
toflag
. If an IRI is used, pass"-I"
toflag
.output_path – The local file path to save the converted ontology to. Will infer format from the extension, otherwise, use the
fmt
param.input_flag – The flag to denote if the file is local or remote. Tries to infer from input string if none is given
merge – Use ROBOT’s merge command to squash all graphs together
fmt – Explicitly set the format
check – By default, the OBO writer strictly enforces document structure rules <http://owlcollab.github.io/oboformat/doc/obo-syntax.html#4>. If an ontology violates these, the convert to OBO operation will fail. These checks can be ignored by setting this to false.
reason – Turn on ontology reasoning
extra_args – Extra positional arguments to pass in the command line
- Returns:
Output from standard out from running ROBOT