rustybam 0.2.0

bioinformatics toolkit in rust
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57

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());
    }
}