Implement a `prepare-corpora` command

monarch-initiative / pheval

A framework for empirical evaluation of phenotype matching and prioritisation

https://monarch-initiative.github.io/pheval/

Apache License 2.0

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Implement a `prepare-corpora` command #311

Closed yaseminbridges closed 4 months ago

yaseminbridges commented 5 months ago

The idea of this utility command is that it will prepare the corpora (phenopackets):

Update the gene identifiers in the phenopacket (if needed)
Remove phenopackets from the corpus that are missing variant information required for spiking into a VCF (if needed)
Spike VCFs into a template VCF (if needed)

The output should be a directory containing a subdirectory of phenopackets that are ready to be used in the pipeline & a subdirectory of VCFs if specified.

matentzn commented 5 months ago

Very very good idea. Thanks!

pheval-utils prepare-corpus

I would suggest to make liberal use of "logging" in there:

When you change values a logger.warning (with the changed values, and the name of the phenopacket)
When you drop a file a strong warning

yaseminbridges commented 5 months ago

Very very good idea. Thanks!

pheval-utils prepare-corpus

I would suggest to make liberal use of "logging" in there:

When you change values a logger.warning (with the changed values, and the name of the phenopacket)

When you drop a file a strong warning

Sounds good, will do!