Nucleotide Models

Nucleotide-focused Python model types for parsed HGVS variants.

Type Aliases:

Name	Description
`NucleotideSequenceItem`	Tagged union for supported inserted or replacement nucleotide sequence models.
`NucleotideEdit`	Tagged union for supported nucleotide edit models.

NucleotideSequenceItem `module-attribute`

NucleotideSequenceItem: TypeAlias = LiteralSequenceItem | RepeatSequenceItem | CopiedSequenceItem

Tagged union for supported inserted or replacement nucleotide components:

NucleotideEdit `module-attribute`

NucleotideEdit: TypeAlias = NucleotideSequenceOmittedEdit | NucleotideSubstitutionEdit | NucleotideInsertionEdit | NucleotideDeletionInsertionEdit | NucleotideRepeatEdit

Tagged union for supported nucleotide edit models:

Allele `dataclass`

Allele(variants: tuple[VariantT, ...])

Bases: Generic[VariantT]

One allele carrying one or more variants in cis.

Attributes:

Name	Type	Description
`variants`	`tuple[VariantT, ...]`	Variants described on the same allele and therefore treated as occurring together in cis.

Examples:

A nucleotide allele carrying multiple variants:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000001.11:g.[123G>A;345del]")
>>> len(variant.description.allele_one.variants)
2

A protein allele carrying multiple variants together:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NP_003997.1:p.[Ser68Arg;Asn594del]")
>>> len(variant.description.allele_one.variants)
2

iter

__iter__() -> Iterator[VariantT]

Return an iterator over variants carried by an allele in order.

Returns:

Type	Description
`Iterator[VariantT]`	Iterator over variants carried by this allele, in the order they appear in the written description.

Examples: >>> from tinyhgvs import parse_hgvs >>> allele = parse_hgvs( ... "NP_003997.1:p.[Ser68Arg;Asn594del]" ... ).description.allele_one >>> len(tuple(allele)) 2

>>> from tinyhgvs import parse_hgvs
>>> allele = parse_hgvs(
...     "NC_000001.11:g.[123G>A;345del]"
... ).description.allele_one
>>> len(tuple(allele))
2

AllelePhase

Bases: str, Enum

Model describing phase between/among alleles.

Attributes:

Name	Type	Description
`TRANS`		Alleles are In-trans phase.
`UNCERTAIN`		Phase between/among alleles is uncertain.

Examples:

In-trans alleles:

>>> from tinyhgvs import parse_hgvs
>>> variants = parse_hgvs("NM_004006.2:c.[2376G>C];[3103del]")
>>> variants.description.phase
<AllelePhase.TRANS: 'trans'>

Uncertain phase:

>>> variant = parse_hgvs("NC_000001.11:g.123G>A(;)345del")
>>> variant.description.phase
<AllelePhase.UNCERTAIN: 'uncertain'>

In-trans protein alleles:

>>> variants = parse_hgvs("NP_003997.1:p.[Ser68Arg];[Ser68=]")
>>> variants.description.phase
<AllelePhase.TRANS: 'trans'>

Protein alleles with uncertain phase:

>>> variant = parse_hgvs("NP_003997.1:p.(Ser73Arg)(;)(Asn103del)")
>>> variant.description.phase
<AllelePhase.UNCERTAIN: 'uncertain'>

AlleleVariant `dataclass`

AlleleVariant(allele_one: Allele[VariantT], allele_two: Allele[VariantT] | None = None, phase: AllelePhase | None = None, alleles_unphased: tuple[Allele[VariantT], ...] = ())

Bases: Generic[VariantT]

Structured representation of HGVS allele variant syntax.

An allele variant may describe:

a single allele carrying one or more variants.
two alleles with an explicit phase relationship.
additional alleles whose relation to the established allele state is uncertain.

Attributes:

Name	Type	Description
`allele_one`	`Allele[VariantT]`	First allele in the allele-variant description.
`allele_two`	`Allele[VariantT] \| None`	Second allele, if present.
`phase`	`AllelePhase \| None`	Phase relation between `allele_one` and `allele_two`. This is `None` when only one allele is described.
`alleles_unphased`	`tuple[Allele[VariantT], ...]`	Additional alleles in uncertain relation to the allele state established by `allele_one` and `allele_two`.

Examples:

Variants in cis on a single allele:

>>> from tinyhgvs import parse_hgvs
>>> desc = parse_hgvs("NC_000023.10:g.[30683643A>G;33038273T>G]").description
>>> len(tuple(desc))
1
>>> desc.allele_two is None
True
>>> desc.phase is None
True
>>> len(desc.allele_one.variants)
2

Two nucleotide alleles in trans:

>>> desc = parse_hgvs("NM_004006.2:c.[2376G>C];[3103del]").description
>>> desc.allele_two is not None
True
>>> desc.phase
<AllelePhase.TRANS: 'trans'>
>>> len(desc.allele_one.variants)
1
>>> len(desc.allele_two.variants)
1

Additional alleles with uncertain phase:

>>> desc = parse_hgvs(
...     "NM_004006.2:c.[296T>G;476T>C];[476T>C](;)1083A>C"
... ).description
>>> desc.phase
<AllelePhase.TRANS: 'trans'>
>>> len(desc.unphased_alleles)
1
>>> len(desc.unphased_alleles[0].variants)
1

Variants in cis on a single protein allele:

>>> desc = parse_hgvs("NP_003997.1:p.[Ser68Arg;Asn594del]").description
>>> len(tuple(desc))
1
>>> desc.allele_two is None
True
>>> desc.phase is None
True
>>> len(desc.allele_one.variants)
2

Two protein alleles in trans:

>>> desc = parse_hgvs("NP_003997.1:p.[Ser68Arg];[Ser68=]").description
>>> desc.allele_two is not None
True
>>> desc.phase
<AllelePhase.TRANS: 'trans'>
>>> len(desc.allele_one.variants)
1
>>> len(desc.allele_two.variants)
1

phased_alleles `property`

phased_alleles: tuple[Allele[VariantT], Allele[VariantT]] | None

Return the established phased allele pair, if present.

Returns:

Type	Description
`tuple[Allele[VariantT], Allele[VariantT]] \| None`	The established phased allele pair as `(allele_one, allele_two)` when this description contains two established alleles with an explicit phase relationship; otherwise, `None`.

Notes

This property reports only the primary phased allele pair represented by allele_one and allele_two. Alleles in alleles_unphased are not included.

Examples:

A single allele does not establish a phased pair:

>>> from tinyhgvs import parse_hgvs
>>> desc = parse_hgvs("NC_000001.11:g.[123G>A;345del]").description
>>> desc.phased_alleles is None
True

Two alleles with established phase return a pair:

>>> desc = parse_hgvs("NM_004006.2:c.[2376G>C];[2376=]").description
>>> desc.phase
<AllelePhase.TRANS: 'trans'>
>>> pair = desc.phased_alleles
>>> pair is not None
True
>>> len(pair[0].variants), len(pair[1].variants)
(1, 1)

Two alleles with uncertain phase do not return a pair:

>>> desc = parse_hgvs("NC_000001.11:g.123G>A(;)345del").description
>>> desc.phase
<AllelePhase.UNCERTAIN: 'uncertain'>
>>> pair = desc.phased_alleles
>>> pair is None
True

Additional alleles with uncertain relation to the established pair:

>>> desc = parse_hgvs(
...     "NM_004006.2:c.[296T>G;476T>C];[476T>C](;)1083A>C"
... ).description
>>> pair = desc.phased_alleles
>>> pair is not None
True
>>> len(desc.alleles_unphased)
1

Two protein alleles with known phase:

>>> desc = parse_hgvs("NP_003997.1:p.[Ser68Arg];[Ser68=]").description
>>> desc.phase
<AllelePhase.TRANS: 'trans'>
>>> pair = desc.phased_alleles
>>> pair is not None
True
>>> len(pair[0].variants), len(pair[1].variants)
(1, 1)

Two predicted protein alleles with unknown phase:

>>> desc = parse_hgvs("NP_003997.1:p.(Ser73Arg)(;)(Asn103del)").description
>>> desc.phase
<AllelePhase.UNCERTAIN: 'uncertain'>
>>> desc.phased_alleles is None
True
>>> len(desc.unphased_alleles)
0

unphased_alleles `property`

unphased_alleles: tuple[Allele[VariantT], ...]

Return alleles with uncertain relation to the allele state established by allele_one and allele_two.

Returns:

Type	Description
`tuple[Allele[VariantT], ...]`	Alleles written after the established allele state whose relation to that state is uncertain. Empty when not present.

Notes

This property exposes the additional alleles stored in alleles_unphased. It does not include allele_one or allele_two.

Examples:

Uncertain phase between two primary alleles does not create an unphased tail:

>>> from tinyhgvs import parse_hgvs
>>> desc = parse_hgvs("NC_000001.11:g.123G>A(;)345del").description
>>> len(desc.unphased_alleles)
0

One additional unphased allele to the established state:

>>> desc = parse_hgvs(
...     "NM_004006.2:c.[296T>G];[476T>C](;)1083A>C"
... ).description
>>> len(desc.unphased_alleles)
1
>>> len(desc.unphased_alleles[0].variants)
1

Multiple additions of unphased alleles to the established state:

>>> desc = parse_hgvs(
...     "NM_004006.2:c.[296T>G];[476T>C](;)1083A>C(;)1406del"
... ).description
>>> len(desc.unphased_alleles)
2

One additional unphased protein allele to the established state:

>>> desc = parse_hgvs("p.[Ser68Arg];[Asn594del](;)0").description
>>> len(desc.unphased_alleles)
1
>>> desc.unphased_alleles[0].variants[0].effect.kind
'no_protein_produced'

No additional unphased protein alleles:

>>> desc = parse_hgvs("NP_003997.1:p.(Ser73Arg)(;)(Asn103del)").description
>>> len(desc.unphased_alleles)
0

iter

__iter__() -> Iterator[Allele[VariantT]]

Iterate over alleles in description order.

Yields:

Type	Description
`Allele[VariantT]`	Alleles in description order: `allele_one`, then `allele_two` when present, followed by any entries in `alleles_unphased`.

Notes

Iteration preserves the structural order of the HGVS allele-variant description. It does not infer or reorder alleles by phase.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> desc = parse_hgvs("NM_004006.2:c.[2376G>C];[3103del]").description
>>> len(tuple(desc))
2

>>> desc = parse_hgvs(
...     "NM_004006.2:c.[296T>G;476T>C];[476T>C](;)1083A>C"
... ).description
>>> len(tuple(desc))
3

>>> desc = parse_hgvs("NP_003997.1:p.[Ser68Arg];[Ser68=]").description
>>> len(tuple(desc))
2

>>> desc = parse_hgvs("p.[Ser68Arg];[Asn594del](;)0").description
>>> len(tuple(desc))
3

NucleotideAnchor

Bases: str, Enum

HGVS reference point used to interpret a nucleotide position.

Attributes:

Name	Type	Description
`ABSOLUTE`		Coordinate is read directly on the named reference sequence.
`RELATIVE_CDS_START`		Coordinate is read relative to the CDS start site.
`RELATIVE_CDS_END`		Coordinate is read relative to the CDS end site.

Examples:

An intronic splice-site substitution uses direct coordinates:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NM_004006.2:c.357+1G>A")
>>> variant.description.location.start.anchor
<NucleotideAnchor.ABSOLUTE: 'absolute'>

A 5' UTR substitution is anchored to the CDS start:

>>> variant = parse_hgvs("NM_007373.4:c.-1C>T")
>>> variant.description.location.start.anchor
<NucleotideAnchor.RELATIVE_CDS_START: 'relative_cds_start'>

A 3' UTR substitution is anchored to the CDS end:

>>> variant = parse_hgvs("NM_001272071.2:c.*1C>T")
>>> variant.description.location.start.anchor
<NucleotideAnchor.RELATIVE_CDS_END: 'relative_cds_end'>

NucleotideCoordinateKind

Bases: str, Enum

Known/unknown state for a nucleotide coordinate.

Attributes:

Name	Type	Description
`KNOWN`		Coordinate has anchor, coordinate, and offset values.
`UNKNOWN`		Coordinate is written as `?`.

NucleotideCoordinate `dataclass`

NucleotideCoordinate(kind: NucleotideCoordinateKind, anchor: NucleotideAnchor | None = None, coordinate: int | None = None, offset: int | None = None)

Nucleotide coordinate written as a known position or ?.

Attributes:

Name	Type	Description
`kind`	`NucleotideCoordinateKind`	Whether this coordinate is known or unknown.
`anchor`	`NucleotideAnchor \| None`	Reference point used to interpret the coordinate. `None` for unknown coordinates.
`coordinate`	`int \| None`	Primary HGVS coordinate as written. `None` for unknown coordinates.
`offset`	`int \| None`	Signed secondary displacement from the primary coordinate. `None` for unknown coordinates. Positive values move downstream and negative values move upstream.

Examples:

Duplication crossing an exon/intron border:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000023.11(NM_004006.2):c.260_264+48dup")
>>> variant.description.location.start.coordinate
260
>>> variant.description.location.end.coordinate
264
>>> variant.description.location.end.offset
48

Upstream intronic substitution:

>>> variant = parse_hgvs("NG_012232.1(NM_004006.2):c.264-2A>G")
>>> variant.description.location.start.coordinate
264
>>> variant.description.location.start.offset
-2

5' UTR substitution:

>>> variant = parse_hgvs("NM_007373.4:c.-1C>T")
>>> variant.description.location.start.anchor
<NucleotideAnchor.RELATIVE_CDS_START: 'relative_cds_start'>
>>> variant.description.location.start.coordinate
-1
>>> variant.description.location.start.offset
0

3' UTR substitution:

>>> variant = parse_hgvs("NM_001272071.2:c.*1C>T")
>>> variant.description.location.start.anchor
<NucleotideAnchor.RELATIVE_CDS_END: 'relative_cds_end'>
>>> variant.description.location.start.coordinate
1
>>> variant.description.location.start.offset
0

5' UTR intronic substitution:

>>> variant = parse_hgvs("NM_001385026.1:c.-106+2T>A")
>>> variant.description.location.start.anchor
<NucleotideAnchor.RELATIVE_CDS_START: 'relative_cds_start'>
>>> variant.description.location.start.coordinate
-106
>>> variant.description.location.start.offset
2

is_known `property`

is_known: bool

Return True when this coordinate has a known value.

is_unknown `property`

is_unknown: bool

Return True when this coordinate is written as ?.

is_intronic `property`

is_intronic: bool

Return True for intronic variant.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NM_004006.2:c.357+1G>A")
>>> variant.description.location.start.is_intronic
True
>>> variant = parse_hgvs("NM_001385026.1:c.-106+2T>A")
>>> variant.description.location.start.is_intronic
True

is_cds_start_anchored `property`

is_cds_start_anchored: bool

Return True if variant's location is relative to the CDS start.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NM_007373.4:c.-1C>T")
>>> variant.description.location.start.is_cds_start_anchored
True
>>> variant = parse_hgvs("NM_001385026.1:c.-106+2T>A")
>>> variant.description.location.start.is_cds_start_anchored
True

is_cds_end_anchored `property`

is_cds_end_anchored: bool

Return True if variant's location is relative to the CDS end.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NM_001272071.2:c.*1C>T")
>>> variant.description.location.start.is_cds_end_anchored
True
>>> variant = parse_hgvs("NM_001272071.2:c.*639-1G>A")
>>> variant.description.location.start.is_cds_end_anchored
True

is_five_prime_utr `property`

is_five_prime_utr: bool

Return True for exonic positions in the 5' UTR.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> position = parse_hgvs("NM_007373.4:c.-123C>T").description.location.start
>>> position.is_five_prime_utr
True
>>> position = parse_hgvs("NM_001385026.1:c.-106+2T>A").description.location.start
>>> position.is_five_prime_utr
False
>>> position.is_three_prime_utr
False

is_three_prime_utr `property`

is_three_prime_utr: bool

Return True for exonic positions in the 3' UTR.

Examples:

>>> from tinyhgvs import parse_hgvs
>>> position = parse_hgvs("NM_001272071.2:c.*1C>T").description.location.start
>>> position.is_three_prime_utr
True
>>> position = parse_hgvs("NM_001272071.2:c.*639-1G>A").description.location.start
>>> position.is_three_prime_utr
False
>>> position.is_five_prime_utr
False

CopiedSequenceItem `dataclass`

CopiedSequenceItem(source_reference: ReferenceSpec | None, source_coordinate_system: CoordinateSystem | None, source_location: Interval[NucleotideCoordinate], is_inverted: bool)

Copied nucleotide sequence used in an insertion or deletion-insertion.

Attributes:

Name	Type	Description
`source_reference`	`ReferenceSpec \| None`	Source reference when the copied sequence comes from a different accession. `None` means the same outer reference.
`source_coordinate_system`	`CoordinateSystem \| None`	Source coordinate system when it differs from the outer variant. `None` means the same outer coordinate system.
`source_location`	`Interval[NucleotideCoordinate]`	Inclusive interval on the source reference.
`is_inverted`	`bool`	Whether the copied sequence is inserted in reverse orientation.

Examples:

A stretch of sequence from the same transcript is inserted in reverse orientation:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NM_004006.2:c.849_850ins850_900inv")
>>> item = variant.description.edit.items[0]
>>> item.is_from_same_reference
True
>>> item.source_location.start.coordinate
850
>>> item.source_location.end.coordinate
900
>>> item.is_inverted
True

A copied sequence can also come from another chromosome:

>>> variant = parse_hgvs("NC_000002.11:g.47643464_47643465ins[NC_000022.10:g.35788169_35788352]")
>>> item = variant.description.edit.items[0]
>>> item.source_reference.primary.id
'NC_000022.10'
>>> item.source_coordinate_system
<CoordinateSystem.GENOMIC: 'g'>

LiteralSequenceItem `dataclass`

LiteralSequenceItem(value: str)

Model describing literal-base-type sequence edit component.

Attributes:

Name	Type	Description
`value`	`str`	Nucleotide bases.

Examples:

A literal insertion of three nucleotides:

>>> from tinyhgvs import LiteralSequenceItem, parse_hgvs
>>> variant = parse_hgvs("NC_000023.10:g.32862923_32862924insCCT")
>>> item = variant.description.edit.items[0]
>>> isinstance(item, LiteralSequenceItem)
True
>>> item.value
'CCT'

RepeatSequenceItem `dataclass`

RepeatSequenceItem(unit: str, count: int)

Model describing repeat-type sequence edit component.

Attributes:

Name	Type	Description
`unit`	`str`	Repeat unit of nucleotide bases.
`count`	`int`	Number of units being repeated.

Examples:

The insertion contains 100 copies of N:

>>> from tinyhgvs import RepeatSequenceItem, parse_hgvs
>>> variant = parse_hgvs("NC_000023.10:g.32717298_32717299insN[100]")
>>> item = variant.description.edit.items[0]
>>> isinstance(item, RepeatSequenceItem)
True
>>> item.unit
'N'
>>> item.count
100

NucleotideRepeatBlock `dataclass`

NucleotideRepeatBlock(count: int, unit: str | None = None, location: Interval[NucleotideCoordinate] | None = None)

One repeat block/unit in a nucleotide repeat description.

Attributes:

Name	Type	Description
`count`	`int`	Number of repeated units.
`unit`	`str \| None`	Literal base(s) repeat unit. None when repeat unit is described in the form of `location[count]`.
`location`	`Interval[NucleotideCoordinate] \| None`	Location per repeat block. None when repeat unit is described in the form of `unit[count]`.

Examples:

A literal 3bp bases repeat with 23 units:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000014.8:g.123CAG[23]")
>>> block = variant.description.edit.blocks[0]
>>> block.unit
'CAG'
>>> block.count
23
>>> block.location is None
True

A RNA repeat variant composed of consecutive repeat units, each described in the form location[count], rather than unit[count]: a repetitive unit from a location:

>>> variant = parse_hgvs("NM_004006.3:r.456_465[4]466_489[9]490_499[3]")
>>> block = variant.description.edit.blocks[1]
>>> block.unit is None
True
>>> block.location.start.coordinate
466
>>> block.location.end.coordinate
489

NucleotideSequenceOmittedEdit

Bases: str, Enum

Nucleotide edits whose altered sequence is not written explicitly.

Attributes:

Name	Type	Description
`NO_CHANGE`		No nucleotide change, written as `=`.
`DELETION`		Deletion of the reference interval, written as `del`.
`DUPLICATION`		Duplication of the reference interval, written as `dup`.
`INVERSION`		Inversion of the reference interval, written as `inv`.

Examples:

A coding DNA deletion:

>>> from tinyhgvs import NucleotideSequenceOmittedEdit, parse_hgvs
>>> variant = parse_hgvs("NM_004006.2:c.5697del")
>>> variant.description.edit is NucleotideSequenceOmittedEdit.DELETION
True

A genomic duplication:

>>> variant = parse_hgvs("NC_000001.11:g.1234_2345dup")
>>> variant.description.edit
<NucleotideSequenceOmittedEdit.DUPLICATION: 'duplication'>

NucleotideSubstitutionEdit `dataclass`

NucleotideSubstitutionEdit(reference: str, alternate: str)

Model describing nucleotide substitution.

Examples:

A reference base C is substituted by A at the described location.

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000023.10:g.33038255C>A")
>>> variant_edit = variant.description.edit
>>> variant_edit.reference
'C'
>>> variant_edit.alternate
'A'
>>> variant_edit.kind
'substitution'

NucleotideInsertionEdit `dataclass`

NucleotideInsertionEdit(items: tuple[NucleotideSequenceItem, ...])

Model describing nucleotide insertion.

Attributes:

Name	Type	Description
`items`	`tuple[NucleotideSequenceItem, ...]`	Inserted sequence items in the order they appear in the HGVS expression.
`kind`	`Literal['insertion']`	Edit kind.

Examples:

Literal nucleotide insertion:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000023.10:g.32862923_32862924insCCT")
>>> variant_edit = variant.description.edit
>>> variant_edit.items[0].value
'CCT'

A composite insertion can mix literal and copied sequence:

>>> variant = parse_hgvs("LRG_199t1:c.419_420ins[T;450_470;AGGG]")
>>> variant_edit = variant.description.edit
>>> len(variant_edit.items)
3
>>> variant_edit.items[0].value
'T'
>>> variant_edit.items[1].is_from_same_reference
True
>>> variant_edit.items[2].value
'AGGG'

Insertion of unspecified repeated bases:

>>> variant = parse_hgvs("NC_000023.10:g.32717298_32717299insN[100]")
>>> variant_edit = variant.description.edit
>>> variant_edit.items[0].unit
'N'
>>> variant_edit.items[0].count
100

NucleotideDeletionInsertionEdit `dataclass`

NucleotideDeletionInsertionEdit(items: tuple[NucleotideSequenceItem, ...])

Model describing nucleotide deletion-insertion.

Attributes:

Name	Type	Description
`items`	`tuple[NucleotideSequenceItem, ...]`	Replacement sequence items in the order they appear in the HGVS expression.
`kind`	`Literal['deletion_insertion']`	Edit kind.

Examples:

A deleted interval is replaced by one literal sequence component.

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("LRG_199t1:c.850_901delinsTTCCTCGATGCCTG")
>>> variant_edit = variant.description.edit
>>> variant_edit.items[0].value
'TTCCTCGATGCCTG'

A deleted interval can be replaced by copied sequence from the same reference:

>>> variant = parse_hgvs("NC_000022.10:g.42522624_42522669delins42536337_42536382")
>>> variant_edit = variant.description.edit
>>> variant_edit.items[0].source_location.start.coordinate
42536337

A deleted interval is replaced by repeated unspecified bases.

>>> variant = parse_hgvs("NM_004006.2:c.812_829delinsN[12]")
>>> variant_edit = variant.description.edit
>>> variant_edit.items[0].unit
'N'
>>> variant_edit.items[0].count
12

NucleotideRepeatEdit `dataclass`

NucleotideRepeatEdit(blocks: tuple[NucleotideRepeatBlock, ...])

Model describing a top-level nucleotide repeat variant.

Attributes:

Name	Type	Description
`blocks`	`tuple[NucleotideRepeatBlock, ...]`	Repeat blocks/units written in the HGVS description.
`kind`	`Literal['repeat']`	Edit kind.

Examples:

A DNA repeat variant with explicit repeat unit:

>>> from tinyhgvs import parse_hgvs
>>> variant = parse_hgvs("NC_000014.8:g.123CAG[23]")
>>> variant_edit = variant.description.edit
>>> variant_edit.blocks[0].unit
'CAG'
>>> variant_edit.blocks[0].count
23

A RNA repeat variant composed of consecutive blocks/units, each represented as a location span:

>>> variant = parse_hgvs("NM_004006.3:r.456_465[4]466_489[9]490_499[3]")
>>> variant_edit = variant.description.edit
>>> len(variant_edit.blocks)
3
>>> variant_edit.blocks[2].count
3

NucleotideVariant `dataclass`

NucleotideVariant(location: Location[NucleotideCoordinate], edit: NucleotideEdit)

Model describing a nucleotide-level variant.

Attributes:

Name	Type	Description
`location`	`Location[NucleotideCoordinate]`	`Location` where the nucleotide edit occurs.
`edit`	`NucleotideEdit`	Nucleotide edit applied at the location.

Examples:

A splice-site substitution is represented by a nucleotide location and a nucleotide substitution edit.

>>> from tinyhgvs import NucleotideSubstitutionEdit, parse_hgvs
>>> variant = parse_hgvs("NM_004006.2:c.357+1G>A")
>>> isinstance(variant.description.edit, NucleotideSubstitutionEdit)
True
>>> variant_description = variant.description
>>> variant_description.location.start.coordinate
357
>>> variant_description.location.start.offset
1

Nucleotide Models

NucleotideSequenceItem module-attribute

NucleotideEdit module-attribute

Allele dataclass

__iter__

AllelePhase

AlleleVariant dataclass

phased_alleles property

unphased_alleles property

__iter__

NucleotideAnchor

NucleotideCoordinateKind

NucleotideCoordinate dataclass

is_known property

is_unknown property

is_intronic property

is_cds_start_anchored property

is_cds_end_anchored property

is_five_prime_utr property

is_three_prime_utr property

CopiedSequenceItem dataclass

LiteralSequenceItem dataclass

RepeatSequenceItem dataclass

NucleotideRepeatBlock dataclass

NucleotideSequenceOmittedEdit

NucleotideSubstitutionEdit dataclass

NucleotideInsertionEdit dataclass

NucleotideDeletionInsertionEdit dataclass

NucleotideRepeatEdit dataclass

NucleotideVariant dataclass

NucleotideSequenceItem `module-attribute`

NucleotideEdit `module-attribute`

Allele `dataclass`

iter

AlleleVariant `dataclass`

phased_alleles `property`

unphased_alleles `property`

iter

NucleotideCoordinate `dataclass`

is_known `property`

is_unknown `property`

is_intronic `property`

is_cds_start_anchored `property`

is_cds_end_anchored `property`

is_five_prime_utr `property`

is_three_prime_utr `property`

CopiedSequenceItem `dataclass`

LiteralSequenceItem `dataclass`

RepeatSequenceItem `dataclass`

NucleotideRepeatBlock `dataclass`

NucleotideSubstitutionEdit `dataclass`

NucleotideInsertionEdit `dataclass`

NucleotideDeletionInsertionEdit `dataclass`

NucleotideRepeatEdit `dataclass`

NucleotideVariant `dataclass`