https://github.com/applicativesystem/rust-bedtools-pangenome
rust-bedtools but from the pangenome point of view.
https://github.com/applicativesystem/rust-bedtools-pangenome
algorithm bedtools bioinformatics bioinformatics-algorithms genome-annotation pangenome pangenome-analysis
Last synced: 3 months ago
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rust-bedtools but from the pangenome point of view.
- Host: GitHub
- URL: https://github.com/applicativesystem/rust-bedtools-pangenome
- Owner: sciencegenome
- License: mit
- Created: 2025-01-05T18:53:58.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-01-15T20:55:33.000Z (4 months ago)
- Last Synced: 2025-01-24T19:37:21.597Z (4 months ago)
- Topics: algorithm, bedtools, bioinformatics, bioinformatics-algorithms, genome-annotation, pangenome, pangenome-analysis
- Language: Rust
- Homepage:
- Size: 6.62 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# rust-bedtools-pangenome
- rust-bedtools but from the pangenome point of view.
- rust ancestral state estimation from genome arthemtic intervals from bed alignment.
- searches for the longest alignment match according to the specified length filter.
- infers the ancestrals states using the prank.
- writes the ancestral states in a separate fasta file.
- general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.
```
cargo build
```
- to run the binary
```
➜ gauravsablok rust-ancestral-state git:(main) ✗
./target/debug/rust-pangenome-ancestral-state -h
Usage: rust-pangenome-ancestral-state
Arguments:
please provide the path to the first alignment file
please provide the alignment length to be used as a threshold
please provide the reference fasta file
Options:
-h, --help Print help
-V, --version Print version
```
```
./target/debug/rust-pangenome-ancestral-state
./sample-file/sample.bed
./sample-file/sample.fasta 7 ./prank
-rw-r--r--. 1 gauravsablok gauravsablok 72 Jan 6 22:10 ancestral-aligned.fasta.best.anc.dnd
-rw-r--r--. 1 gauravsablok gauravsablok 104 Jan 6 22:10 ancestral-aligned.fasta.best.anc.fas
-rw-r--r--. 1 gauravsablok gauravsablok 66 Jan 6 22:10 ancestral-aligned.fasta.best.fas
```
Gaurav Sablok