Note: This is Offsetbasedgraph version 2.1, made to work with Graph Peak Caller. For the version compatible with the analysis done in the paper Coordinates and Intervals in Graph-based Reference Genomes, go to version 1.0.7.

Offsetbasedgraph

This is a python package for working with and representing genomic graphs without sequence in Python. Together with pyvg, Offsetbasedgraph can be used to represent graphs created by vg.

Installation

Offsetbasedgraph version 2.0 is compatible with Python 3 only. Install with pip:

pip3 install offsetbasedgraph

... or by cloning:

git clone https://github.com/uio-cels/OffsetBasedGraph.git
cd OffsetBasedGraph
pip3 install -e .

Basic usage

Graphs can be created by sending a dict of Blocks (connected nodes) and dict of edges (one list of edges per key node) to the Graph object.

from offsetbasedgraph import Graph, Block
graph = Graph({1: Block(10), 2: Block(5)}, {1: [2]})

An interval contain a start offset, end offset and a list of blocks it follows:

from offsetbasedgraph import Interval
interval = Interval(3, 6, [1, 2], graph)

Offsetbasedgraph can be used together with pyvg to represent huge graphs created by vg (requires vg json graph format):

from pyvg.conversion import json_file_to_obg_numpy_graph
offset_based_graph = json_file_to_obg_numpy_graph("vggraph.json")