gnomAD (The Genome Aggregation Database) is aggregation of thousands of exomes and genomes human sequencing studies. Also, gnomAD consortium annotates the variants with allelic frequency in genomes and exomes. Here, this batch script is able to search the genes or transcripts of your interest and retrieve variant data from the database via gnomAD backend API that based on GraphQL query language.
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Create a directory and download the "gnomad_python_api.py" and "requirements.txt" files or clone the repository via Git using following command:
git clone https://github.com/furkanmtorun/gnomad_python_api.git -
Install the required packages if you do not already:
pip3 install -r requirements.txt -
It's ready to use now!
If you did not install pip yet, please follow the instruction here.
| Options in the script | Description | Parameters |
|---|---|---|
| -filter_by | It defines the input type | gene_name, gene_id, transcript_id |
| -search_by | It defines the input | Type a gene/transcript identifier e.g.: TP53, ENSG00000169174, ENST00000544455 Type the name of file containig your inputs e.g: myGenes.txt |
| -dataset | It defines the dataset | exac, gnomad_r2_1, gnomad_r3, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed |
| -h | It displays the parameters | To get help via script: python gnomad_python_api.py -h |
- How to list the variants by gene name or gene id?
python gnomad_python_api.py -filter_by="gene_name" -search_by="TP53" -dataset="gnomad_r2_1"
Here, "gene_id" can also be used instead of "gene_name" after stating an Ensembl Gene ID instead of a gene name.
- How to list the variants by transcript ID?
python gnomad_python_api.py -filter_by="transcript_id" -search_by="ENST00000544455" -dataset="gnomad_r3"
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How to list the variants using a file containing genes/transcripts?
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Prepare your file that contains gene name, Ensembl gene IDs or Ensembl transcript IDs line-by-line.
ENSG00000169174
ENSG00000171862
ENSG00000170445 -
Then, run the following command:
python gnomad_python_api.py -filter_by="gene_id" -search_by="myFavoriteGenes.txt" -dataset="exac" -
Please, use only one type of identifier in the file.
- Then, the variants will be listed in "outputs" folder in the files according to their identifier (gene name, gene id or transcript id).
- That's all!
I would be very happy to see any feedbacks and contributions on the script.
Furkan Torun | [email protected] | Web site: furkanmtorun.github.io