Check if scoring files are in PGS Catalog format with JSON schema

[nebfield]

combine_scorefiles should check that input files meet the PGS Catalog standard to detect if custom scoring files are able to be combined with PGS Catalog data

[smlmbrt]

@ens-lgil do we have anything that would do this already? Or perhaps rolling in some of the validators to here could be useful in the future?

[ens-lgil]

Not really. We use pandas_schema (from the GWAS validator): https://github.com/PGScatalog/pgs_scoringfile_validator/blob/master/validator/validate/schema.py

And I used a slightly simplified version for the harmonized validator: https://github.com/ens-lgil/pgs_harmonizedfile_validator/blob/main/validator/validate/schema.py

[ens-lgil]

However, including the different PGS scoring file validators into pgscatalog_utils would make sense.

[smlmbrt]

However, including the different PGS scoring file validators into pgscatalog_utils would make sense.

I think it would make sense to explore including them as a validation module within this package?

[ens-lgil]

Potentially something close to what we have currently here for the harmonized files: https://github.com/ens-lgil/pgs_harmonizedfile_validator And we can include/integrate the validator of the formatted scoring files

[smlmbrt]

Related functionality added in #22