This repository contains code supporting the paper Coordinates and Intervals on Offset-based graphs. See the section "How to run the gene experiments" for information about how to run the gene experiments.
For a demo of the interactive web tool, please follow this link: http://46.101.93.163/gen-graph-coords/
The module requires Python3 and pip3 (which should be included with Python) in order to install dependencies.
There is one dependency:
- The python package offsetbasedgraph. Install it with
pip3 install offsetbasedgraph.
Install the above requirements. Then clone this repo:
git clone https://github.com/uio-cels/genomicgraphcoords.git
In this experiment, we create a simple graph from GRCh38 by merging the "flanking regions" of the alternatice loci with the main path. We then represent refseq genes on this graph, and investigate the relationship between transcripts on the alternative loci and the main chromosomes. The following steps will reproduce the experiment:
# Create grch38 graph with translation object.
python3 gen_graph_coords.py create_graph data/grch38.chrom.sizes data/grch38_alt_loci.txt grch38.graph
# Analyse genes
python3 gen_graph_coords.py check_duplicate_genes grch38.graph data/genes/genes_refseq.txt
In this experiment, we create a more complex graph by merging parts of the alternative loci, using alignments generated by NCBI. We then investigate the relationship between transcripts on the alternative loci and main chromosomes using multi-path intervals.
The following will reproduce the experiment for fuzzy multi-path intervals:
python3 gen_graph_coords.py analyse_multipath_genes data/grch38.chrom.sizes data/grch38_alt_loci.txt data/alt_alignments/ data/genes/genes_refseq.txt fuzzy
Using critical-interval multi-path intervals :
python3 gen_graph_coords.py analyse_multipath_genes data/grch38.chrom.sizes data/grch38_alt_loci.txt data/alt_alignments/ data/genes/genes_refseq.txt critical