All Pairs Shortest Paths

The APSP algorithm is also a pathway reconstruction algorithm that connects every source to every target, returning the induced edge subnetwork from these paths.

Usage

usage: allpairs.py [-h] --network NETWORK --nodes NODES --output OUTPUT [--directed | --no-directed]
allpairs.py: error: the following arguments are required: --network, --nodes, --output

Where:

• network is a weighted tsv edgelist (source, target, weight)
• nodes is a no-header tsv of node names and their type (source/target)
• output is the place to output the subnetwork
• --directed/--no-directed specifies whether the interactome is fully undirected or fully directed.