mg-rest-tad

Microservice RESTful API for the querying of a Cassandra db that had been generated using the code from the mg-process-fastq scripts

Requirements

• Cassandra 3.7+
• Python 2.7+ (If using Cassandra 3.7 this requires Python 2.7.10 or less)
• pyenv
• pyenv virtualenv
• pip
• Python Modules
  • Flask
  • Flask-Restful
  • json
  • pytest
  • cassandra
  • elasticsearch
  • MySQLdb

Installation

Initialise

pyenv virtualenv TADrest

cd rest

Require data files

The dataset files for each of the genomes:

• datasets.json

{
    "taxon_id": {
        "9606": {
            "accession": {
                "GCA_000001405.22": {
                    "datasets": ["rao2014"],
                    "chromosomes": [
                        ["1", 249250621],
                        ["2", 243199373],
                        ["3", 198022430],
                        ["4", 191154276],
                        ["5", 180915260],
                        ...
                    ]
                }
            }
        }
    }
}

Starting the Service

virtualenv env
source env/bin/activate

cd rest
python app.py

Place this in the boot scripts to get intialised as a service.

RESTful API

List taxon IDs

wget http://<host>/rest/v0.0/getTADs/

List assemblies

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>

List options for the assembly

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>/<string:accession_id>

List datasets

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>/<string:accession_id>/datasets

List available resolutions

List the avaiable resolutions the are loaded for a given dataset

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>/<string:accession_id>/resolutions

List chromosomes

List the chromosomes at the given resolution

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>/<string:accession_id>/chromosomes

List TADs

List the TADs for a given taxon and assembly that match the defined conditions within the parameters

wget http://<host>/rest/v0.0/getTADs/<string:taxon_id>/<string:accession_id>/tads?chr=<string:chromosome_id>&res=<integer:resolution>&start=<integer:start_pos>&end=<integer:end_position>

All of the parameters are required. If one or more of chr, res, start or end are missing then an exception is raised