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codonpdx-python

Build Status

Pythond Backend Celery Tasks

  • Mirroring and Provisioning
  • Codon Counter / Ratio Calculations
  • PostgreSQL Interface

Cloning This Repository

git clone git@github.com:PDX-Flamingo/codonpdx-python.git

Setup

Create a PyPy virtualenv and then run the following commands.

source .venv/bin/activate
pip install -r requirements.txt
make

Configuration

There are several configuration files that need to be configured before use.

Sample configuration files are provided for the following:

  • config/db.cfg
  • config/mirror.cfg
  • config/codonpdx.cfg
  • codonpdx/celeryconfig.py

Usage

Starting a celery worker

This will start a celery worker which is used by the webapp and mirror command.

celery -A codonpdx worker -l info

The celery worker can also be daemonized.

Mirroring and Provisioning Metadata

Wiki

Codon Count

generate codon count metadata for a file

zcat ~/refseq/release/complete/complete.1.genomic.gbff.gz| ./codonpdx.py count -f genbank > /tmp/complete.1.json

Wiki

Insert

load count metadata into refseq

cat /tmp/complete.1.json | ./codonpdx.py insert -d refseq

Calc

calculate scores for NG_027788.1

./codonpdx.py calc -d refseq -v NG_027788.1

Wiki

Results

DataSet Version OS Compiler Python codonpdx Jobs Time
refseq Release 65 CentOS 6 GCC 4.9.0 PyPy 2.31 v1.0.0 32 12.35 minutes
genbank Release 201 CentOS 6 GCC 4.9.0 PyPy 2.31 v1.0.0 32 95.20 minutes