https://github.com/combat-tb/vcf2neo

A tool to import SnpEff annotated files to a Neo4j Graph database
https://github.com/combat-tb/vcf2neo

graph-database neo4j-database py2neo snpeff tuberculosis variant-calling

Last synced: about 1 month ago
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A tool to import SnpEff annotated files to a Neo4j Graph database

• Host: GitHub
• URL: https://github.com/combat-tb/vcf2neo
• Owner: COMBAT-TB
• License: gpl-3.0
• Created: 2017-01-12T07:13:50.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2022-12-08T05:10:46.000Z (about 2 years ago)
• Last Synced: 2023-05-20T14:29:14.645Z (over 1 year ago)
• Topics: graph-database, neo4j-database, py2neo, snpeff, tuberculosis, variant-calling
• Language: Python
• Homepage:
• Size: 38.1 MB
• Stars: 3
• Watchers: 8
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# vcf2neo

[![Build Status](https://travis-ci.org/COMBAT-TB/vcf2neo.svg?branch=master)](https://travis-ci.org/COMBAT-TB/vcf2neo)

[![Coverage Status](https://coveralls.io/repos/github/COMBAT-TB/vcf2neo/badge.svg?branch=master)](https://coveralls.io/github/COMBAT-TB/vcf2neo?branch=master)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1219127.svg)](https://doi.org/10.5281/zenodo.1219127)

A tool to import and map **[SnpEff annotated](http://snpeff.sourceforge.net/SnpEff.html)** VCF files to [COMBAT-TB NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) Graph database.

**Prerequisites**:

- [`docker`](https://docs.docker.com/v17.12/install/) and [`docker-compose`](https://docs.docker.com/compose/install/) :whale:

## Usage

**Clone repository**:

```sh

$ git clone https://github.com/SANBI-SA/vcf2neo.git

...

$ cd vcf2neo

```

**Build [COMBAT-TB NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb)**:

```sh

$ docker-compose up --build -d

...

```

**Install and run `vcf2neo`**:

- Using `pip`

```sh

$ pip install -i https://test.pypi.org/simple/ vcf2neo

...

```

- or via `setup` in `virtualenv`

```sh

$ virtualenv envname

...

$ source envname/bin/activate

$ pip install -r requirements.txt

$ python setup.py install

```

**Import and map SnpEff annotated VCF files to genes and drugs in NeoDB**:

You change the default database location (`localhost`) by setting the

`DATABASE_URL` environment variable to `remote`.

```sh

$ vcf2neo load_vcf --help

Usage: vcf2neo load_vcf [OPTIONS] VCF_DIR

  Load SnpEff annotated VCF files to genes and drugs in NeoDb.

Options:

  --owner TEXT                    Specify owner.  [default: $USER; required]

  -p, --phenotype [XDR|MDR|SUSCEPTIBLE|UNKNOWN]

                                  Specify phenotype.  [required]

  -a, --antibiotic TEXT           Specify antibiotic. E.g. Rifampicin

                                  [required]

  --help                          Show this message and exit.

```

```sh

$ vcf2neo load_vcf -p UNKNOWN -a UNKNOWN PATH/TO/VCF_DIR

...

```

**Exploring variant data**:

Point your browser to [localhost:7474](http://0.0.0.0:7474) to access the Neo4j browser.

To view the schema, run:

```cql

call db.schema.visualization

```

Sample [Cypher](https://neo4j.com/developer/cypher-query-language/) query:

```cql

MATCH(g:Gene)--(v:Variant)--(cs:CallSet)

RETURN g.name as gene, v.consequence as variant, cs.name as file

LIMIT 25

```