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https://github.com/dubssieg/rs-pancat-compare
Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
https://github.com/dubssieg/rs-pancat-compare
distance distance-calculation distance-measures graph-distance pangenome pangenome-graph pangenomics variation-graph variation-graphs
Last synced: 18 days ago
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Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
- Host: GitHub
- URL: https://github.com/dubssieg/rs-pancat-compare
- Owner: dubssieg
- License: agpl-3.0
- Created: 2024-09-06T15:47:43.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2024-11-19T09:26:23.000Z (25 days ago)
- Last Synced: 2024-11-19T10:30:35.232Z (25 days ago)
- Topics: distance, distance-calculation, distance-measures, graph-distance, pangenome, pangenome-graph, pangenomics, variation-graph, variation-graphs
- Language: Rust
- Homepage:
- Size: 1.12 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-pangenomes - rs-pancat-compare
README
# Pairwise edit distance between pangenome graphs
> [!NOTE]\
> [pancat compare](https://github.com/Tharos-ux/pancat) is a tool, originally written in Python, designed to compute a distance between pangenome graphs made from a same group of genomes. For performance, it has been reimplemented in Rust.
Program that calculates the distance between two GFA (Graphical Fragment Assembly) files. It takes in the file paths of the two GFA files. The program first identifies the common paths between the two graphs by finding the intersection of their path names. For each common path, the program reads those and output differences in segmentation in-between them. The purpose is to output the necessary operations (merges and splits) required to transform the graph represented by the first GFA file into the graph represented by the second GFA file.
## Install instructions:
Requires rust and cargo.
```bash
git clone
cd rs-pancat-compare
cargo build
```
## Usage
```bash
./target/debug/rs-pancat-compare graph_A.gfa graph_B.gfa > output.tsv
```
:warning: Only accept P-lines as paths in GFA files - please convert your GFA1.1 files to GFA1.0 with vg for instance.
| Organism | Chromosom | Wall time | Memory |
|----------|-----------|-----------|--------|
| yeast | 1 | 0.56s | 3.0MB |
| human | 21 | 5m08s | 383MB |
| human | 1 | 17m42s | 1.2GB |
Timings and peak memory usage over diverse datasets. Jobs executed on a single core of a 13th Gen Intel® Core™ i7-1365U @ 3.6GHz.
> [!NOTE]\
> Want to contribute? Feel free to open a PR on an issue about a missing, buggy or incomplete feature! **Please do bug reports in the issue tracker!**.
## Output
Program outputs to `stdout` in a `.tsv` format editions as well as informations about the comparison.
```
# Intersection of paths: [pathname:str,+]
## pathname:str pathlength:int
# Path name Position Operation NodeA NodeB BreakpointA BreakpointB
pathname:str [0-9]+:int [M|S]:str [0-9]+:str [0-9]+:str [0-9]+:int [0-9]+:int
...
# Distance: [0-9]+:int (E=[0-9]+:int, S=[0-9]+:int, M=[0-9]+:int).
```
Output features:
+ Lines starting with '#' are comments or information about the comparison
+ Lines starting with '##' are haplotypes length information
+ Every other line is either a merge (M) or a split (S)
+ Equivalences are accounted in the final line but not written as output (too many in file)
+ Distance is the sum of merges and splits
+ `Path name` is the haplotype name string
+ `Position` is the global position on the graph the edit takes place
+ `NodeA` (resp. `NodeB`) is the node on pathA (resp. pathB) where the edition occurs
+ `BreakpointA` (resp. `BreakpointB`) is the next breakpoint position on pathA (resp. pathB)