Dna.get_annotations

missionbio.mosaic.dna.Dna.get_annotations

Dna.get_annotations(variants: Optional[Sequence] = None, genome: Optional[str] = None) → DataFrame

Annotate DNA variants.

Annotates the ids of the assay (of form chrA-B-C-D), where A,B,C,D represent the chromosome, position, reference, and alternate variant values of an arbitrary length. The annotation is pulled using the Mission Bio annotation API. It consists of attributes such as Coding Impact, DANN score, Gene and Protein name, dbSNP IDs etc.

Note

A direct connection to https://api.missionbio.io is needed to download variant annotations. While proxy support has been added to our wish list, the current version does not support it. Use a network that does not require a proxy. Alternatively, ask your network admin to add firewall rules that allow direct connections to https://api.missionbio.io.

Parameters:

variantslist

Variant ids to get annotations for (e.g. [‘chr1:12341234:T/A’]). By default, it will get annotations for all variants from the assay.

genomestr

The genome version to use for annotation. By default, it will use the genome version in the assay metadata. Example, “hg19” and “hg38”.

Returns:

pd.DataFrame:

The indices are the variant ids and columns are the various annotation attributes

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< Class Dna