networker 0.1.0

a python package to generate and analyse protein similarity networks

networker

Description

This repository contains scripts to create and analyse protein (or nucleotide) identity networks.

Scirpts

1. networker.py

Usage:

python networker.py proteinseqs.faa

or,

python networker.py diamondorblastdatabase.tsv

If provided with a DIAMOND or BLAST table (.tsv), or an amino acid fasta file (.faa) 'networker.py' will produce a protein/nucleotide identity network ('xxx.html') and a list of nodes used in the network ('xxx.txt').

It is recommended that you use .faa as an input, however if you want to use your own table, the file must have the format: qseqid | sseqid | pident

For example, to make a usable DIAMOND search:

diamond makedb --db example --in example.faa

diamond blastp --db example --query example.faa --out example.tsv --outfmt 6 qseqid sseqid pident

All steps are currently automatic, including thresholding. However, the recommended threshold should work for most putposes. In future, you will be able to provide a custom threshold.

2. subnetworker.py

WIP

3. histogramer.py

WIP

Example Data

Example data and output can be found in the example_data folder. The file example.faa was used to generate the DIAMOND database and, subsequentally, the network ('example.html') and the node list ('example.txt').

To Do

1. Enable custom thresholds.
2. Create 'histogramer.py' to assist with threshold analysis.
3. Create 'subnetworker.py' for analysing subnetworks.
4. Compile into software package.