gene_list_svc

Database cli to get bed files from gene/region lists for different diagnostics

💬 Introduction

Cli implemented in golang to add and update databases for AML and ALL with relevant genes, transcripts, exons or genetic regions, extract all potential fusion partners for certain genes (http://atlasgeneticsoncology.org/), get genetic coordinates from the ENSEMBL api and write .bed files for different analyses and diagnostics.

❗ Dependencies

To use the cli, the following dependencies must be met:

🔧 Configuration

Env	Required	Default
DB_HOST	-	localhost
DB_PORT	-	5432
DB_USER	x	-
DB_PASSWORD	x	-
DB_NAME	-	gene_list
ATLAS_ROOT_URL	-	http://atlasgeneticsoncology.org
ENSEMBL_38_REST_URL	-	https://rest.ensembl.org
ENSEMBL_37_REST_URL	-	https://grch37.rest.ensembl.org

🏁 Flags

  -analysis string
    	Select analysis (snv, cnv, sv, pindel).
  -bed string
    	Output bed file name (default: [list]_[analysis]_[build].bed).
  -build string
    	Select genome build (37, 38; default: 38).
  -list string
    	Select gene list (aml, aml_ext, all).
  -tsv string
    	Path to tsv file containing gene list.

🚀 Usage

Start docker containers - Still under development - no docker available yet!

To use this cli, a postgres database server is needed and start the cli docker with an interactive session:

docker run -d -e POSTGRES_PASSWORD=notsosecret postgres
docker run -it --rm marrip/gene_list_svc:latest bash

Input `.tsv` file

To load new data into the database, compile a .tsv file like so:

BCR	Gene	snv	aml	Specific
KMT2A	Gene	sv	all	All
RUNX1	Gene	snv,sv,cnv	aml,all	Specific
...

Adding data to database

To add data from a .tsv file, simply run:

gene_list_svc -tsv /path/to/data.tsv

Retrieve data and write to bed file

Choose analysis, diagnostic route, genome build and desired .bed file name to retrieve data from the database:

gene_list_svc -list aml -analysis snv -build 38 -bed /path/to/aml_snv_38.bed

marrip/gene_list_svc