- 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 <ALIGNMENT> <THRESHOLD> <FASTAFILE>
Arguments:
<ALIGNMENT> please provide the path to the first alignment file
<THRESHOLD> please provide the alignment length to be used as a threshold
<FASTAFILE> 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