README.md

dotty - cdot-based position projection

What can it do?

Run it the background, e.g., from main as

$ DATA_DIR=$PWD/data \
    pipenv run uvicorn dotty.main:app --host 0.0.0.0 --port 8080 --reload

Then, resolve c./n./g. variants to SPDI-like variants

$ curl 'http://127.0.0.1:8080/api/v1/to-spdi?q=NM_000059.3:c.274G%3EA' 2>/dev/null | jq .
{
  "spdi": {
    "assembly": "GRCh38",
    "contig": "13",
    "pos": 32319283,
    "reference_deleted": "C",
    "alternate_inserted": "A"
  }
}

Obtaining Data

datasets is the NCBI datasets tool.

$ mkdir -p data
$ cd data

$ wget \
    https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch37.json.gz \
    https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch38.json.gz \
    https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch37.json.gz \
    https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch38.json.gz

$ download genome accession GCF_000001405.25 --filename GRCh37.zip
$ download genome accession GCF_000001405.40 --filename GRCh38.zip
$ unzip GRCh37.zip
$ unzip GRCh38.zip
$ seqrepo --root-directory $PWD load --namespace ncbi --instance-name seqrepo ncbi_dataset/data/GCF_000001405.*/*.fna
$ rm -rf GRCh3?.zip ncbi_dataset

Dump OpenAPI Schema

# python -m dotty.main > openapi.yaml