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Unsupported Syntax

tinyhgvs parses supported HGVS syntax into structured Rust and Python models. For a small set of recognized HGVS families that are not modeled yet, parsing raises a structured unsupported-syntax error instead of a generic syntax error.

Unsupported diagnostic codes begin with unsupported.. The current active unsupported families are listed below.

What Error To Expect

Python:

from tinyhgvs import TinyHGVSError, parse_hgvs

try:
    parse_hgvs("NC_000023.11:g.pter_qtersup")
except TinyHGVSError as error:
    print(error.kind.value)
    print(error.code)
    print(error.fragment)

Expected output:

unsupported_syntax
unsupported.telomeric_position
pter

Rust:

let error = tinyhgvs::parse_hgvs("NC_000023.11:g.pter_qtersup").unwrap_err();
assert_eq!(error.code(), "unsupported.telomeric_position");
assert_eq!(error.fragment(), Some("pter"));

unsupported.telomeric_position

Telomeric DNA coordinate syntax is recognized but not modeled yet.

Examples:

  • NC_000023.11:g.pter_qtersup
  • NC_000002.12:g.pter_8247756delins[NC_000011.10:g.pter_15825266]

Expected error:

kind: unsupported_syntax
code: unsupported.telomeric_position
fragment: pter or qter

unsupported.epigenetic_edit

DNA epigenetic edit modifiers are recognized but not modeled yet.

Example:

  • NC_000011.10:g.1999904_1999946|gom

Expected error:

kind: unsupported_syntax
code: unsupported.epigenetic_edit
fragment: |gom

unsupported.rna_adjoined_transcript

RNA adjoined transcript syntax is recognized but not modeled yet.

Examples:

  • NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
  • NM_152263.2:r.-115_775::aggcucccuugg::NM_002609.3:r.1580_*1924

Expected error:

kind: unsupported_syntax
code: unsupported.rna_adjoined_transcript
fragment: ::

unsupported.rna_splicing_outcome

Some higher-level RNA splicing outcome containers remain unsupported. Direct RNA outcomes such as r.?, r.(?), r.0, r.0?, and r.spl are supported. Derived RNA allele forms such as r.[897u>g,832_960del] are also supported.

Example:

  • NC_000023.11(NM_004006.2):r.(897u>g,832_960del)

Expected error:

kind: unsupported_syntax
code: unsupported.rna_splicing_outcome
fragment: r.(...)