mygfa

This is a simple Python library for parsing, manipulating, and emitting pangenomic graphs in the GFA format. It prioritizes simplicity and clarity over performance and functionality.

As demonstrated in example.py, this is what it looks like to compute the node depth for a GFA file:

import mygfa
import sys
graph = mygfa.Graph.parse(sys.stdin)
seg_depths = {name: 0 for name in graph.segments}
for path in graph.paths.values():
    for step in path.segments:
        seg_depths[step.name] += 1

Type pip install mygfa to get started.