PGScatalog / pgscatalog_utils

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files
Apache License 2.0
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effect_weight column changes format #39

Closed smlmbrt closed 1 year ago

smlmbrt commented 1 year ago

Related to: https://github.com/PGScatalog/pgsc_calc/issues/79

Debugging the scorefile (PGS002678) yields some sort of mismatched schema:

AssertionError: MISMATCHED SCHEMA
Current columns: {'ID': <class 'polars.datatypes.Utf8'>, 'effect_type': <class 'polars.datatypes.Categorical'>, 'chr_position': <class 'polars.datatypes.UInt64'>, 'accession': <class 'polars.datatypes.Categorical'>, 'matched_effect_allele': <class 'polars.datatypes.Categorical'>, 'chr_name': <class 'polars.datatypes.Categorical'>, 'effect_weight': <class 'polars.datatypes.Utf8'>}
Correct schema:{'chr_name': <class 'polars.datatypes.Categorical'>, 'chr_position': <class 'polars.datatypes.UInt64'>, 'ID': <class 'polars.datatypes.Utf8'>, 'matched_effect_allele': <class 'polars.datatypes.Categorical'>, 'effect_weight': <class 'polars.datatypes.Float64'>, 'effect_type': <class 'polars.datatypes.Categorical'>, 'accession': <class 'polars.datatypes.Categorical'>}