ga4gh / vrs-python

GA4GH Variation Representation Python Implementation
https://github.com/ga4gh/vrs
Apache License 2.0
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feat!: declare annotator CLI as console entrypoint #447

Closed jsstevenson closed 2 months ago

jsstevenson commented 2 months ago

Declare the annotator click function as a console entry point, enabling vrs-annotate input.vcf --vcf_out=out.vcf rather than python3 src/ga4gh/vrs/extras/vcf_annotation.py input.vcf --vcf_out=out.vcf.

Open to suggestions on the command name. I'd prefer a structure more along the lines of vrs-annotate vcf input.vcf --vcf_out=out.vcf (i.e., vrs-annotate is the command, vcf is a subcommand) if we think there's a chance that other filetypes could be annotated in the future (in that case, we may want to alter the module name as well). Alternatively, though, the subcommand might be superfluous if the file argument has a suffix indicating the filetype.

jsstevenson commented 2 months ago

initial feelings seem to be supportive of vcf subcommand to vrs-annotate