anyvar.translate.base
Provide base properties for Translator classes.
- exception anyvar.translate.base.TranslationError[source]
Indicates failure to translate provided term into known variation structure.
- class anyvar.translate.base.Translator[source]
Base Translator class.
Use for * Translating incoming variant expressions to VRS * Acquiring reference accessions for incoming sequence descriptions/references
- abstractmethod get_sequence_id(accession_id)[source]
Get GA4GH sequence identifier for provided accession ID
- Parameters:
accession_id (
str) – ID to convert- Return type:
str- Returns:
equivalent GA4GH sequence ID
- Raise:
KeyError if no equivalent ID is available
- abstractmethod translate_allele(var)[source]
Translate provided variation text into a normalized VRS object.
- Parameters:
var (
str) – user-provided string describing or referencing a variation.- Return type:
Allele|CopyNumberChange|CopyNumberCount|None- Returns:
VRS variation object if able to normalize
- Raises:
TranslatorConnectionError – if translation request returns error
- abstractmethod translate_cnv(var)[source]
Translate provided variation text into a normalized VRS object.
- Parameters:
var (
str) – user-provided string describing or referencing a variation.- Return type:
Allele|CopyNumberChange|CopyNumberCount|None- Returns:
VRS variation object if able to normalize
- Raises:
TranslatorConnectionError – if translation request returns error
- abstractmethod translate_variation(var, **kwargs)[source]
Translate provided variation text into a VRS Variation object.
- Parameters:
var (
str) – user-provided string describing or referencing a variation.- Kwargs:
input_type (types.VrsVariation): The type of variation for var. If not provided, will first try to translate to allele and then copy number
copies (int) - The number of copies for VRS Copy Number Count
copy_change (models.CopyChange) - The EFO code for VRS COpy Number Change
assembly_name(str) -> Assembly name for
var. Only used whenvaruses gnomad format. Defaults to “GRCh38”. Must be “GRCh38” or “GRCh37”. VRS-Python sets a default, but we should set a default just in case VRS-Python ever changes the default.
- Return type:
Allele|CopyNumberChange|CopyNumberCount- Returns:
VRS variation object
- Raises:
TranslationError – if translation is unsuccessful, either because the submitted variation is malformed, or because VRS-Python doesn’t support its translation.