A RecMap object can be created from reading in a HapMap-formatted recombination map. Note that since the HapMap recombination format does not include the chromosome lengths, this must be specified too. A convenience function read_seqlens is provided to read in TSV-formatted "genome" files of the chromosome names and lengths.
Here is a example which loads a recombination map from a HapMap-formatted recombination map and calculates the total map lengths.
use recmap::prelude::*;
let seqlens = read_seqlens("hg38_seqlens.tsv")
.expect("could not read seqlens");
let rec_map = RecMap::from_hapmap("decode_2019_map.txt", seqlens)
.expect("cannot read hapmap");
for (name, rate_map) in rec_map.iter() {
println!("{}\t{}", name, rate_map.total_map_length().unwrap());
}
This example can be run on the command line with:
cargo run --example calc_map_lengths -- --seqlens hg38_seqlens.tsv decode_2019_map.txt
One of the most common tasks when working with recombination maps is to estimate the map position of arbitrary markers, which is usually done by linear interpolation. RecMap provides an easy way to do this for one position (RecMap.interpolate_map_position()) and for many positions, with RecMap.interpolate_map_positions():
use recmap::prelude::*;
let seqlens = read_seqlens("hg38_seqlens.tsv")
.expect("could not read seqlens");
let rec_map = RecMap::from_hapmap("decode_2019_map.txt", seqlens)
.expect("cannot read hapmap");
let positions = vec![11975064, 15007450];
rec_map.interpolate_map_positions("chr1", &positions);
Additionally, recmap had an optional command line tool feature that interpolates recombination map positions and recombination rates, given BED3 input:
$ recmap interp --seqlens hg38_seqlens.tsv --hapmap decode_2019_map.txt \
hg38_1Mb_windows.bed --output decode_2019_map_1Mb_summaries.tsv --header
Currently the command line tool only has one subcommand, though more features may be added. Please file an issue if there is a feature you'd like!
To use the library in your own Rust projects, install with:
$ cargo add recmap
To install the command line tool, use:
$ cargo install recmap --features=cli
15 Dec 23, 2022
35 Apr 8, 2023
30 Dec 7, 2022
57 Nov 20, 2022
110 Dec 25, 2022
776 Jan 1, 2023
9 Oct 10, 2022
256 Dec 27, 2022
219 Dec 31, 2022
5 Aug 20, 2022
12 Feb 25, 2024
3 Nov 2, 2023
4 Oct 24, 2022
4 Jul 18, 2022
3 Aug 17, 2023
104 Oct 7, 2023
4 Dec 16, 2022
3 Jan 3, 2023
16 Nov 12, 2022