overview.rst

Module Overview

Module	Classes	Description
Variant Object Representation
hgvs.edit	hgvs.edit.AAExt hgvs.edit.AAFs hgvs.edit.AARefAlt hgvs.edit.AASub hgvs.edit.Dup hgvs.edit.Edit hgvs.edit.NACopy hgvs.edit.NADupN hgvs.edit.NARefAlt hgvs.edit.Repeat	hgvs.edit classes implement various kinds of sequence edits. For nucleic acids, these edits are independent of location; amino acids edits currently contain the location.
hgvs.hgvsposition	hgvs.hgvsposition.HGVSPosition	A non-standard representation of a sequence location without an edit. For example, NM_012345.6:c.72+5_73-2.
hgvs.location	hgvs.location.AAPosition hgvs.location.BaseOffsetPosition hgvs.location.Interval hgvs.location.SimplePosition	Various kinds of locations. Interval is a span from start to end; the others are points in a sequence.
hgvs.posedit	hgvs.posedit.PosEdit	A position+edit (really, an interval and edit).
hgvs.variant	hgvs.variant.SequenceVariant	A sequence variant of any type (g, c, m, r, n, p). A SequenceVariant is returned by hgvs.parser.Parser, and it is the input and output type for hgvs.variantmapper.VariantMapper operations.
Parsing and Formatting
hgvs.parser	hgvs.parser.Parser
*Coordinate, Interval, and Variant Mappin	g/Transformation*
hgvs.projector	hgvs.projector.Projector
hgvs.alignmentmapper	hgvs.alignmentmapper.AlignmentMapper
hgvs.variantmapper	hgvs.variantmapper.VariantMapper hgvs.assemblymapper.AssemblyMapper
Variant Normalization and Validation
hgvs.normalizer	hgvs.normalizer.Normalizer
hgvs.validator	hgvs.validator.Validator hgvs.validator.IntrinsicValidator hgvs.validator.ExtrinsicValidator
External Data Providers
hgvs.dataproviders.interface	hgvs.dataproviders.interface.Interface
hgvs.dataproviders.uta	hgvs.dataproviders.uta.UTABase