`dnadrive` is a tool to convert data to and from the openMoSS format
Python HTML
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
dnadrive
templates
.gitignore
DNA3.jpg
Dockerfile
README.md
dnadriveTest.py
fileToFasta.py
licence.txt
requirements.txt
server.py
setup.cfg
setup.py
uwsgi.ini

README.md

DNAdrive

dnadrive is a tool to convert data to and from the openMoSS format. please see the Techinical Documentation for more details.

See the demo here

Installation

  • pip install dnadrive (or)
  • Please install in a virtualenv that is running python2.7 (we do not support python3 as of now)
  • python setup.py install in the source directory will also install
  • pip install -r requirements.txt if you would like to use the provided flask server. (does not install with pip)

Usage

All supported operations are done on files

  • -e or -d encodes/decodes the file
  • -i and -o provide the input and ouput paths
  • -v let's you choose the openmoss variant from
  • variant is detected automatically on decode

Variant list to choose from

  1. Cost efficiency - GCGGGGCXXXXCGGGGCG
  2. Balanced - CGGGGCXXXXCGGGGC
  3. Lower secondary structures - CGGGGXXXXGGGGC
  4. No secondary structures - GGGGXXXXGGGG
  • To Encode
dnadrive  -e -i input.test -o output.test -v 1
  • To Decode
dnadrive  -d -i output.test -o check.test 
  • To Generate Well File
dnadrive  -g -i output.test -o check.test 

DOCKER

we provide a docker file for REST access to openmoss encoding/decoding service.

docker build -t helix-dnadrive .
docker run -d -p 5000:5000 helix-dnadrive

API EXAMPLES

curl -X POST -F filedata=@input.png --data "variant=1" "http://localhost:5000/encode/" > out.moss

curl -X POST -F filedata=@out.moss "http://localhost:5000/decode/" > out.png

LICENCE

The Project is available under the MIT licence. see licence.txt for more information.

This software is in pre-alpha stage and the APIs are not set in stone and may change without notice. please contact wingston@helix.works for any help you may need in getting the platform set up.

Forks will be avaluated and merged on their own merit. so please feel free to hack away at the platform.