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use super::*;
use bio::alphabets::dna::revcomp;
use bio_types::strand::Strand::{Forward, Reverse};
use rust_htslib::faidx;
use std::str;
pub fn fetch_fasta(reader: &faidx::Reader, chrom: &str, start: usize, end: usize) -> Vec<u8> {
let seq = reader.fetch_seq(chrom, start, end).unwrap().to_owned();
seq
}
/// # Example
/// ```
/// use rustybam::getfasta::get_fasta;
/// get_fasta(".test/test.fa", ".test/getfasta.bed", true, true);
/// get_fasta(".test/test.fa", ".test/getfasta.bed", false, true);
/// get_fasta(".test/test.fa", ".test/getfasta.bed", true, false);
/// get_fasta(".test/test.fa", ".test/getfasta.bed", false, false);
/// get_fasta(".test/test.fa.gz", ".test/getfasta.bed.gz", true, false);
/// ```
pub fn get_fasta(path: &str, bed: &str, add_name: bool, use_strand: bool) {
let bed_recs = bed::parse_bed(bed);
let reader = faidx::Reader::from_path(path).unwrap();
// iterate over be records
for rec in bed_recs {
let mut name = format!("{}:{}-{}", rec.name, rec.st, rec.en);
let mut seq = fetch_fasta(&reader, &rec.name, rec.st as usize, rec.en as usize);
// add name information if present
if add_name {
if let Some(n) = rec.record.name() {
name = format!("{}::{}", n, name)
}
}
// add the stand information if present
if use_strand {
match rec.record.strand() {
Some(strand) => {
match strand {
Reverse => {
seq = revcomp(seq);
name.push_str("(-)");
}
Forward => {
name.push_str("(+)");
}
_ => {
name.push_str("(.)");
}
};
}
None => name.push_str("(.)"),
};
}
println!(">{}\n{}", name, str::from_utf8(&seq).unwrap());
}
}