agtools: Tools for manipulating assembly graphs

This repo contains useful scripts to manipulate assembly graph files from different assemblers.

Currently, I have added code for SPAdes (including metaSPAdes) assembly graphs.

Requirements

You should have Python and the following packages installed.

collections - Usually installed by default with Python
re - Usually installed by default with Python
python-igraph

Demo

Please see demo.py for an example.

from agtools.spades_graph_utils import get_graph

def main():
    assembly_graph_file = "tests/data/assembly_graph_with_scaffolds.gfa"
    contig_paths_file = "tests/data/contigs.paths"

    (assembly_graph, contigs_map, contig_names) = get_graph(
        assembly_graph_file, contig_paths_file
    )

    # Total number of vertices
    print(f"Total number of vertices in the assembly graph: {assembly_graph.vcount()}")

    # Total number of edges
    print(f"Total number of edges in the assembly graph: {assembly_graph.ecount()}")

    # Iterate through the contigs
    for i in range(assembly_graph.vcount()):
        # Get neighbours of each contig
        neighbours = assembly_graph.neighbors(i, mode="all")

        # Print ID, contig label and number of neighbours
        print(
            assembly_graph.vs[i]["id"], assembly_graph.vs[i]["label"], len(neighbours)
        )


if __name__ == "__main__":
    main()

You can run demo.py as follows.

python demo.py

You will get assembly_graph which is an igraph.Graph object. You can get more details from the official python-igraph documentation.

Vini2/agtools

agtools: Tools for manipulating assembly graphs

Requirements

Demo