uab-cgds-worthey/DITTO-API
This is the API for serving up DITTO scores and hosting on Cloud.rc at UAB.
DITTO-API
!!! For research purposes only !!!
Repo for querying DITTO predictions for variants using FastAPI.
Requirements
Following are required:
Installing
1. Clone the repository - change in to directory of your choice and run:
git clone https://github.com/uab-cgds-worthey/DITTO-API.git2. Navigate to the project directory
cd DITTO-API3. Build the Docker image
docker build -t ditto-api .4. Run the Docker container
docker run -p 8000:8000 --name ditto-api ditto-api5. Use this link in your browser to retrieve DITTO scores
http://localhost:8000/docs
and use this variant as example: 1-2406483-C-G
Expected result
DITTO will output deleterious score by Ensemble transcript. Below is the output for the above test variant. To verify
the scores, please query the variant in the DITTO web app.
{
"scores_by_transcript": {
"ENST00000288774.7": {
"gene": "PEX10",
"consequence": "intron_variant,splice_site_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
},
"ENST00000447513.6": {
"gene": "PEX10",
"consequence": "intron_variant,splice_site_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
},
"ENST00000507596.5": {
"gene": "PEX10",
"consequence": "intron_variant,splice_site_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
},
"ENST00000510434.1": {
"gene": "PEX10",
"consequence": "2kb_downstream_variant,NMD_transcript_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
},
"ENST00000378513.7": {
"gene": "RER1",
"consequence": "2kb_downstream_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
},
"ENST00000605895.6": {
"gene": "RER1",
"consequence": "2kb_downstream_variant",
"chrom": "chr1",
"pos": "2406483",
"ref_base": "C",
"alt_base": "G",
"DITTO": "1.0"
}
}
}Contributing
We welcome contributions! See the docs for guidelines.
Contact information
For issues, please send an email with clear description to
| Name | |
|---|---|
| Tarun Mamidi | tmamidi@uab.edu |
| Brandon Wilk | bwilk777@uab.edu |