Happie

Happie is a wrapper for several independent programs used to identify different mobile elements.

Context independent Regions

These regions are interesting in and of themselves for what genes they carry, etc

Phages

ProphET

Plasmids

mlplasmids

Genomic Islands

CAFE

Context-dependedt Regions

These regions are short, and are interestesitng solely because of their context

Insertion Sequnes

OASIS

Install

Happie can manually be installed from github as follows

git clone https://github.com/nickp60/happie
cd happie
conda create -n happie  biopython pyyaml
source activate happie
python setup.py install
happy_install_or_update

That is going to take care of downloading Docker images for ProphET, prokka, mlplasmids, dimob.

Running

(Optional) get some test data:

bash ./get_test_data.sh

And try running it!

happie --contigs ./test_data/ecoli104.fna  --output tmpresults

You should get an output file of

Note

This module was renamed from “mobilephone”, it was just too hard to google.