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tb2neo\n\n[![Build Status](https://travis-ci.org/COMBAT-TB/tb2neo.svg?branch=master)](https://travis-ci.org/COMBAT-TB/tb2neo) [![Coverage Status](https://coveralls.io/repos/github/COMBAT-TB/tb2neo/badge.svg?branch=master)](https://coveralls.io/github/COMBAT-TB/tb2neo?branch=master)\n\nParses _M.tuberculosis_ annotation (GFF file) and builds a Neo4j graph\ndatabase storing the annotated features. _tb2neo_ also aggregates and maps\nthese annotated features to external services such as UniProt, CheMBL,\nDrugBank, KEGG, Reactome, QuickGo, STRING-DB etc.\n\n## Usage\n\n### Neo4j Installation\n\n- Instructions for a standalone Neo4j installation can be found [here](https://neo4j.com/docs/operations-manual/current/installation/).\n\n- Using [Docker](https://docs.docker.com/):\n\n    ```sh\n    $ docker run -d -p 7474:7474 -p 7687:7687 --name neo -e NEO4J_AUTH=none -v=$HOME/neo4j/data:/data neo4j:3.5\n    ...\n    ```\n\n### `tb2neo` Installation\n\n- Using `pip`:\n\n    ```sh\n    $ pip install -i https://test.pypi.org/simple/ tb2neo\n    ...\n    ```\n\n- Using `setup`:\n\n    Clone repository and create a virtual environment:\n\n    ```sh\n    $ git clone https://github.com/COMBAT-TB/tb2neo.git\n    ...\n    $ cd tb2neo\n    $ virtualenv envname\n    $ source envname/bin/activate\n    $ pip install -r requirements.txt\n    $ python setup.py install\n    ```\n\n### Loading TB Data\n\nTo load TB data, we use the H37Rv GFF3 file from [EnsemblBacteria](https://bacteria.ensembl.org/Mycobacterium_tuberculosis_h37rv/Info/Index/).\n\nRun the following command to see available options\n\n```sh\n$ tb2neo --help\n...\n```\n\nRun the following command to load GFF features to Neo4j\n\n```sh\n$ tb2neo load_gff --gff_files PATH/TO/TB_GFF3_FILES\n...\n```\n\n### Exploring TB data\n\nPoint your browser to [localhost:7474](http://localhost:7474]).\n\n```cql\ndb.schema()\n```\n\n![DB_MODEL](./images/neodbschema.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Ftb2neo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcombat-tb%2Ftb2neo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Ftb2neo/lists"}