Validation and Normalization¶
hgvs.validator
¶
implements validation of hgvs variants
-
class
hgvs.validator.
ExtrinsicValidator
(hdp, strict=True)[source]¶ Bases:
object
Attempts to determine if the HGVS name validates against external data sources
hgvs.normalizer
¶
hgvs.normalizer
-
class
hgvs.normalizer.
Normalizer
(hdp, cross_boundaries=False, shuffle_direction=3, alt_aln_method='splign', validate=True)[source]¶ Bases:
object
Perform variant normalization
Initialize and configure the normalizer
Parameters: - hdp – HGVS Data Provider Interface-compliant instance
(see
hgvs.dataproviders.interface.Interface
) - cross_boundaries – whether allow the shuffling to cross the exon-intron boundary
- shuffle_direction – shuffling direction
- alt_aln_method – sequence alignment method (e.g., splign, blat)
- validate – whether validating the input variant before normalizing
- hdp – HGVS Data Provider Interface-compliant instance
(see