tseemann / fripan

Interactive, web tool for exploring pan-genome of bacterial strains

FriPan

Introduction

FriPan is a web-based tool for exploring the pan-genome of multiple bacterial genomes. FriPan does not perform the ortholog clustering itself, but it can import data from ProteinOrtho5 output files. Each isolate/strain is a row, and there is a columnar position for each gene cluster. You can zoom/scroll through the pan-proteome, and hover over sections to see a description of the gene.

Installation

Ensure you have browserify installed:

npm install -g browserify

Install the code and build

git clone https://github.com/drpowell/FriPan
cd FriPan
npm install webworkify coffeeify
make compile

Run the demo code: make demo ./server.sh firefox http://localhost:8030/pan.html

Instead of using the provided Python-based server in server.sh you can put it all in your public_html folder if you are running Apache already.

make install  # will put in $HOME/public_html/fripan
firefox http://localhost/~user/fripan/pan.html

Input file

An example ProteinOrtho5 result is provided: pan.proteinortho.example and pan.descriptions.example .

To view results just rename them pan.proteinortho and pan.descriptions. You can view other files by naming them with a consistent stem, for example my-pan1.proteinortho and my-pan1.descriptions. Then you view them by using the url pan.html?my-pan1. Note the suffix of the filenames are important.

It is also possible to give arbitrary information on strains for sorting or colouring. See the pan.strains.example file for an example. This is expected to be a tab separated file with the first column named "ID" with the strain names matching those in pan.proteinortho. Create such a tab separated file and put name it pan.strains.

Development

While developing code, it is useful to enable coffee in "watch" mode and with source maps. Run the following:

coffee -c -w -m *.coffee

Source

• Github: https://github.com/drpowell/FriPan
• Website: http://drpowell.github.io/FriPan/