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 |