| 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 |
|
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 |
|
|
| Coordinate, Interval, and Variant Mapping/Transformation |
hgvs.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
|
|