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phenopackets / phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.
http://phenopackets.org/phenopacket-tools/stable/
GNU General Public License v3.0
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Add InterpretationConverter interface and implement for CLI #29

Closed julesjacobsen closed 1 year ago

julesjacobsen commented 3 years ago

Need a way of extracting v1 disease, gene and variant into a v2 interpretation.

Enable this in CLI convert will need to implement the interface and assume single gene-disease-variant associations or else die.

pnrobinson commented 2 years ago

@julesjacobsen given the lack of semantics for v1, I wonder if it would be better to suggest to users that they extend the example in the CLI to their needs rather than releasing code that might not be correct for some use cases?

ielis commented 2 years ago

Now we have an option to do this in V1toV2Converter.

The functionality is available in CLI via --convert-variants option:

cat phenopacket.v1.json | pxf-tools convert --convert-variants > phenopacket.v2.json