iseqpharmgkb

Name	iseqpharmgkb JSON
Version	0.0.9 JSON
	download
home_page	https://gitlab.com/intelliseq/iseqpharmgkb
Summary	Package for creating database from PharmGKB and querying for specific variant/allele
upload_time	2023-09-27 13:50:33
maintainer
docs_url	None
author	Mateusz Marynowski, Olaf Tomaszewski
requires_python	>=3.6
license
keywords
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # ISEQPHARMGKB

Scripts that allow you to:
1) Create databases (clinical and variant) from [PharmGKB](https://www.pharmgkb.org/) 
2) Get clinical or variant annotations from PharmGKB for own queries

## Install iseqpharmgkb library

Optional steps (create virtual environment):
```
python3 -m venv venv
source venv/bin/activate
```

Obligatory steps:
```
python3 -m pip install --upgrade pip
pip install iseqpharmgkb
```

## Requirements

- python >=3.6
- pandas >= 1.2.4
- requests >= 2.22.0
- SQLAlchemy >= 1.3.17

## Create databases

```
create_database
```

## Get clinical annotations

```
get_clinical_annotation --queries /path/to/query.json --output-filename /output/filename.json
```

An example `query.json` file should look like this:
```
{
    "rs1050828": "CC",
    "rs5030868": "CC",
    "CYP2D6*2": "*2",
    "CYP2D6*1": "*1/*1"
}
```

## Get variant annotations

```
get_variant_annotation --queries /path/to/query.json --output-filename /output/filename.json
```

An example `query.json` file should look like this:
```
{
    "rs1050828": "CC",
    "rs5030868": "CC",
    "CYP2D6*2": "*2",
    "CYP2D6*1": "*1/*1"
}
```

            

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