Name: OffsetBasedGraph
Owner: Centre for Computational Inference in Evolutionary Life Science
Description: Python package for handling genomic offset-based graphs
Created: 2016-09-20 13:37:54.0
Updated: 2017-05-24 12:17:35.0
Pushed: 2018-01-10 08:15:25.0
Homepage: null
Size: 135277
Language: Python
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Note: This is Offsetbasedgraph version 2.0, 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.
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.
Offsetbasedgraph version 2.0 is compatible with Python 3 only. Install with pip:
install offsetbasedgraph
… or by cloning:
clone https://github.com/uio-cels/OffsetBasedGraph.git
ffsetBasedGraph
install -e .
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.
offsetbasedgraph import Graph, Block
h = Graph({1: Block(10), 2: Block(5)}, {1: [2]})
An interval contain a start offset, end offset and a list of blocks it follows:
offsetbasedgraph import Interval
rval = 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):
pyvg.conversion import json_file_to_obg_numpy_graph
et_based_graph = json_file_to_obg_numpy_graph("vggraph.json")