search

EBIvariation / opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB
Apache License 2.0
1 stars 1 forks source link

Issues 26 & 29: Split pgxCategory and report consequences for ref/ref #32

Closed apriltuesday closed 6 months ago

apriltuesday commented 6 months ago

Closes #26, closes #29.

New counts for exploded pgxCategory are displayed like so (taken from tests):

Total clinical annotations: 10
    With RS: 9 (90.00%)
        1. Exploded by allele: 30 (3.3x)
        2. Exploded by PGx category: 33 (1.1x)
        3. Exploded by drug: 69 (2.1x)
        4. Exploded by phenotype: 81 (1.2x)
Total evidence strings: 84
    With CHEBI: 66 (78.57%)
    With EFO phenotype: 33 (39.29%)
    With functional consequence: 57 (67.86%)
    With VEP gene: 57 (67.86%)
Gene comparisons per annotation
    With PGKB genes: 8 (80.00%)
    With VEP genes: 6 (60.00%)
    PGKB genes != VEP genes: 8 (80.00%)
Total RS: 9
    With parsed alleles: 7 (77.78%)
        With >2 alleles: 1 (14.29%)