uta_tools

Service for querying the UTA database

Installation

pip

pip install uta_tools

Development

Clone the repo:

git clone https://github.com/cancervariants/uta_tools
cd uta_tools

Install Pipenv if necessary.

Install backend dependencies and enter Pipenv environment:

pipenv shell
pipenv lock && pipenv sync

UTA Database Installation

uta_tools uses intalls local UTA database. For other ways to install, visit biocommons.uta.

Local Installation

The following commands will likely need modification appropriate for the installation environment.

1. Install PostgreSQL

2. Create user and database.

   $ createuser -U postgres uta_admin
   $ createuser -U postgres anonymous
   $ createdb -U postgres -O uta_admin uta
   

3. To install locally, from the uta_tools/data directory:

export UTA_VERSION=uta_20210129.pgd.gz
curl -O http://dl.biocommons.org/uta/$UTA_VERSION
gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433

Connecting to the database

To connect to the UTA database, you can use the default url (postgresql://uta_admin@localhost:5433/uta/uta_20210129). If you use the default url, you must either set the password using environment variable UTA_PASSWORD or setting the parameter db_pwd in the UTA class.

If you do not wish to use the default, you must set the environment variable UTA_DB_URL which has the format of driver://user:pass@host/database/schema.

Data Downloads

SeqRepo

uta_tools relies on seqrepo, which you must download yourself.

From the root directory:

cd uta_tools
pip install seqrepo
mkdir -p data/seqrepo
seqrepo -r data/seqrepo pull -i 2021-01-29
sudo chmod -R u+w data/seqrepo
cd data/seqrepo
seqrepo_date_dir=$(ls -d */)
sudo mv $seqrepo_date_dir latest

transcript_mappings.tsv

uta_tools uses Ensembl BioMart to retrieve uta_tools/data/transcript_mappings.tsv. We currently use Human Genes (GRCh38.p13) for the dataset and the following attributes we use are: Gene stable ID, Gene stable ID version, Transcript stable ID, Transcript stable ID version, Protein stable ID, Protein stable ID version, RefSeq match transcript (MANE Select), Gene name.

LRG_RefSeqGene

uta_tools fetches the latest version of LRG_RefSeqGene. This file is found can be found here.

MANE Summary Data

uta_tools fetches the latest version of MANE.GRCh38.*.summary.txt.gz. This file is found can be found here.

Init coding style tests

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

• Check code style
• Check for added large files
• Detect AWS Credentials
• Detect Private Key

Before first commit run:

pre-commit install

Testing

From the root directory of the repository:

pytest