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https://github.com/combat-tb/tb2neo
A tool to aggregate and load TB data to Neo4j
https://github.com/combat-tb/tb2neo
genome-annotation gff3 neo4j py2neo tuberculosis
Last synced: about 1 month ago
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A tool to aggregate and load TB data to Neo4j
- Host: GitHub
- URL: https://github.com/combat-tb/tb2neo
- Owner: COMBAT-TB
- License: gpl-3.0
- Created: 2017-07-27T10:12:42.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-12-08T04:49:37.000Z (about 2 years ago)
- Last Synced: 2023-05-20T14:29:14.674Z (over 1 year ago)
- Topics: genome-annotation, gff3, neo4j, py2neo, tuberculosis
- Language: Python
- Homepage:
- Size: 6.94 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# tb2neo
[](https://travis-ci.org/COMBAT-TB/tb2neo) [](https://coveralls.io/github/COMBAT-TB/tb2neo?branch=master)
Parses _M.tuberculosis_ annotation (GFF file) and builds a Neo4j graph
database storing the annotated features. _tb2neo_ also aggregates and maps
these annotated features to external services such as UniProt, CheMBL,
DrugBank, KEGG, Reactome, QuickGo, STRING-DB etc.
## Usage
### Neo4j Installation
- Instructions for a standalone Neo4j installation can be found [here](https://neo4j.com/docs/operations-manual/current/installation/).
- Using [Docker](https://docs.docker.com/):
```sh
$ docker run -d -p 7474:7474 -p 7687:7687 --name neo -e NEO4J_AUTH=none -v=$HOME/neo4j/data:/data neo4j:3.5
...
```
### `tb2neo` Installation
- Using `pip`:
```sh
$ pip install -i https://test.pypi.org/simple/ tb2neo
...
```
- Using `setup`:
Clone repository and create a virtual environment:
```sh
$ git clone https://github.com/COMBAT-TB/tb2neo.git
...
$ cd tb2neo
$ virtualenv envname
$ source envname/bin/activate
$ pip install -r requirements.txt
$ python setup.py install
```
### Loading TB Data
To load TB data, we use the H37Rv GFF3 file from [EnsemblBacteria](https://bacteria.ensembl.org/Mycobacterium_tuberculosis_h37rv/Info/Index/).
Run the following command to see available options
```sh
$ tb2neo --help
...
```
Run the following command to load GFF features to Neo4j
```sh
$ tb2neo load_gff --gff_files PATH/TO/TB_GFF3_FILES
...
```
### Exploring TB data
Point your browser to [localhost:7474](http://localhost:7474]).
```cql
db.schema()
```
