Note
Want to contribute? Feel free to open a PR on an issue about a missing, buggy or incomplete feature!
Tool to analyse shared sequences between populations in pangenomes. This small command-line tool aims to check regions in a graph that are shared by a collection of genomes, and that are not traversed by another collection.
It can extract:
- Nodes that matches a criterion
- Genomic intervals on each sequences
- Bubbles with intervals
Note
Bubbles detection is made possible thanks to BubbleGun, Fawaz Dabbaghie, Jana Ebler, Tobias Marschall, BubbleGun: enumerating bubbles and superbubbles in genome graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4217–4219, https://doi.org/10.1093/bioinformatics/btac448
Installation is made using pip with the provided setup.py file.
git clone https://github.com/Tharos-ux/sharepg.git
git pull
pip install --upgrade pip
python -m pip install .Once installed, command-line become available out-of-the-box. You can check everything went well by printing the manpage with sharepg -h.
Let's assume you happen to have:
- a GFA graph, uncompressed or not
- a list A of paths/walks names you want to follow (g0, g1, g2)
- a list B of paths/walks names you want to avoid (g3, g4)
- a reference name (g0)
- you want to strictly have all paths/walks you follow and not any of the ones you want to avoid (threshold=1.)
# Extract nodes
sharepg disnodes graph.gfa -a g0 g1 g2 -b g3 g4 -r g0 -t 1 > disnodes.log
# Extract intervals
sharepg disintervals graph.gfa -a g0 g1 g2 -b g3 g4 -r g0 -t 1 > disintervals.log
# Extract bubbles
sharepg disbubbles graph.gfa -a g0 g1 g2 -b g3 g4 -r g0 -t 1 > disbubbles.logNote
Threshold parameter is a float within range 0. to 1.; it represents the minimum proportion of genomes that needs to be in A and in the observed region and 1-threshold maximum proportion of genomes of B that can go through this same region. For instance, a threshold of 1. says that for a segment to be selected it needs to have all genomes of A and no genomes from B. A threshold of .7 says that at least 70% of A must go through the region and at most 30% of B can go through he region for it to be selected.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent