gitter-lab / influenza-pb2

Analysis of influenza PB2 protein interactions

FloPro

FloPro is a flow program. This repository is a supplement to our manuscript:

Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus. Steven F Baker, Helene Meistermann, Manuel Tzouros, Aaron Baker, Sabrina Golling, Juliane Siebourg Polster, Mitchell P Ledwith, Anthony Gitter, Angelique Augustin, Hassan Javanbakht, Andrew Mehle. PLoS Biology, 20:12, 2022.

Contents

• code: a Python library and scripts for network flow and enrichment analysis
• condor: scripts for running the analyses in a HTCondor cluster
• data: source and target gene lists for the network flow analysis

System dependencies

• Currently only Linux is officially supported and this package requires graphviz for some of its features, particularly the visualization of sets of enriched genes.

Install python dependencies

We have tested Python >= 3.8, but other Python 3's may work as well.

# setup virtual environment for flopro dependencies
python -m venv env
source env/bin/activate

# install dependencies
pip install -r requirements.txt

# install flopro
cd code/python
python setup.py install

Download data dependencies

cd ../../data
wget -O edges_file.txt https://figshare.com/ndownloader/files/38264646
wget -O mapping_file.txt https://figshare.com/ndownloader/files/38264649

Run flopro

# back to repo root
cd ../
mkdir flow_results
python code/python/scripts/flow.py --min-sources 1 --min-targets 1 --edges-file data/edges_file.txt --mapping-file data/mapping_file.txt --sources-file data/hf_curve_shape_ensp_stringdb_filter.txt --targets-file data/gene_lists/mehle_targets_ensp.txt --outdir flow_results