2 releases
0.1.1 | Sep 12, 2024 |
---|---|
0.1.0 | Sep 11, 2024 |
#247 in Biology
29 downloads per month
Used in abpoa-rs
655KB
6K
SLoC
abPOA Rust Bindings
Adaptive-band partial order alignment in Rust
Installation
Cargo package
TODO
Building from source
Rust compiler
The minimum supported Rust version is 1.80.
Building abPOA
-
Clone the repository.
git clone https://github.com/broadinstitute/abpoa-rs
-
Move into the directory.
cd abpoa-rs
-
Build using
cargo
. We enable a flag to ensure the compiler uses all features of your machine's CPU. To maximize portability of the binary, however, remove theRUSTFLAGS="..."
part.RUSTFLAGS="-C target-cpu=native" cargo build --release
Supported features
- Global, local, and semi-global alignment
- Configuring linear, gap-affine, and convex aligment penalties
- Compututing one or more consensus sequences
- Generating row-column MSA FASTA output
- Importing a POA graph from a FASTA file
Features not yet supported:
- "Strand ambiguous" alignment (on the roadmap)
- Guide-tree supported alignment
- Minimizer-based seeding and alignment
Usage
// Configure the alignment parameters
let aln_params = AlignmentParametersBuilder::new()
.alignment_mode(AlignmentMode::Global)
.gap_affine_penalties(0, 4, 6, 2)
.verbosity(Verbosity::None)
.build();
// Create a new empty POA graph
let mut graph = Graph::new(&aln_params);
let test_seq: Vec<&[u8]> = vec![
b"ACGTGTACAGTTGAC",
b"AGGTACACGTTAC",
b"AGTGTCACGTTGAC",
b"ACGTGTACATTGAC",
];
// Align and add each sequence to the graph
for (i, seq) in test_seq.iter().enumerate() {
let weights = vec![1; seq.len()];
let result = graph
.align_and_add_sequence(&aln_params, seq, &weights, format!("seq{}", i + 1).as_bytes())
.unwrap();
eprintln!("Sequence {}: score = {}", i + 1, result.get_best_score());
}
// Compute the row-column MSA output
graph.generate_rc_msa();
let msa = graph.get_msa();
assert_eq!(msa.len(), 4);
let truth = [
b"ACGTGTACAGTTGAC",
b"A--GGTACACGTTAC",
b"A-GTGTCACGTTGAC",
b"ACGTGTACA-TTGAC",
];
for (i, seq) in msa.sequences().iter().enumerate() {
// The sequence in the MSA object is coded, so we use `reverse_seq` to convert it to ASCII.
let ascii = aln_params.reverse_seq(seq);
assert_eq!(&ascii, truth[i]);
}
// Generate consensus
graph.generate_consensus(ConsensusAlgorithm::HeaviestBundle);
let consensus = graph.get_consensus().unwrap();
let ascii = aln_params.reverse_seq(consensus.sequences().iter().next().unwrap());
eprintln!("Consensus: {}", std::str::from_utf8(ascii).unwrap());
Dependencies
~0.8–3MB
~58K SLoC