Struct bio::io::bed::Record

pub struct Record { /* private fields */ }

A BED record as defined by BEDtools (http://bedtools.readthedocs.org/en/latest/content/general-usage.html)

Implementations

impl Record

pub fn new() -> Self

Create a new BED record.

pub fn chrom(&self) -> &str

Chromosome of the feature.

pub fn start(&self) -> u64

Start position of feature (0-based).

pub fn end(&self) -> u64

End position of feature (0-based, not included).

pub fn name(&self) -> Option<&str>

Name of the feature.

pub fn score(&self) -> Option<&str>

Score of the feature.

pub fn strand(&self) -> Option<Strand>

Strand of the feature.

pub fn aux(&self, i: usize) -> Option<&str>

Access auxilliary fields after the strand field by index (counting first field (chromosome) as 0).

pub fn set_chrom(&mut self, chrom: &str)

Set chromosome.

pub fn set_start(&mut self, start: u64)

Set start of feature.

pub fn set_end(&mut self, end: u64)

Set end of feature.

pub fn set_name(&mut self, name: &str)

Set name.

pub fn set_score(&mut self, score: &str)

Set score.

pub fn push_aux(&mut self, field: &str)

Add auxilliary field. This has to happen after name and score have been set.

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Record

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for Record

fn default() -> Record

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for Record

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl<'a> From<&'a Record> for Contig<String, Strand>

fn from(rec: &Record) -> Self

Returns a Contig annotation for the BED record.

use bio::io::bed;
use bio_types::annot::contig::Contig;
use bio_types::strand::Strand;
let example = b"chr1\t5\t5000\tname1\t0.5";
let mut reader = bed::Reader::new(&example[..]);
let rec = reader
    .records()
    .next()
    .expect("Found no bed record.")
    .expect("Got a csv::Error");
let loc = Contig::from(&rec);
assert_eq!(loc.to_string(), "chr1:5-5000");

impl<R, S> From<Contig<R, S>> for Record where
    R: Deref<Target = str>,
    S: Into<Strand> + Copy, 

Generate a BED format Record for the location.

As created, it will have an empty name.

fn from(contig: Contig<R, S>) -> Self

Performs the conversion.

impl<R, S> From<Pos<R, S>> for Record where
    R: Deref<Target = str>,
    S: Into<Strand> + Copy, 

Generate a BED format Record for an annotation position.

This record will have length 1, and when created it will have an empty name.

fn from(pos: Pos<R, S>) -> Self

Performs the conversion.

impl<R, S> From<Spliced<R, S>> for Record where
    R: Deref<Target = str>,
    S: Into<Strand> + Copy, 

Generate a BED format Record for the position.

Splicing information will be represented with the 12-column BED format, using columns 10 through 12 (blockCount, blockSizes, and blockStarts) for exons.

As created, it will have an empty name and default to using the overall start & end (columns 1 and 2) for the start and end of the “thick” region (columns 7 and 8).

use bio::io::bed;
use bio_types::annot::spliced::{Spliced, SplicingError};
use bio_types::annot::AnnotError;
use bio_types::strand::ReqStrand;
let tad3 = Spliced::with_lengths_starts(
    "chrXII".to_owned(),
    765265,
    &vec![808, 52, 109],
    &vec![0, 864, 984],
    ReqStrand::Reverse,
)
.expect("Encountered a bio_types::annot::spliced::SplicingError.");
assert_eq!(
    tad3.to_string(),
    "chrXII:765265-766073;766129-766181;766249-766358(-)"
);
let tad3_exons = tad3.exon_contigs();
assert_eq!(tad3_exons.len(), 3);
assert_eq!(tad3_exons[0].to_string(), "chrXII:766249-766358(-)");
assert_eq!(tad3_exons[1].to_string(), "chrXII:766129-766181(-)");
assert_eq!(tad3_exons[2].to_string(), "chrXII:765265-766073(-)");
let mut buf = Vec::new();
{
    let mut writer = bed::Writer::new(&mut buf);
    let mut tad3_bed = bed::Record::from(tad3);
    tad3_bed.set_name("YLR316C");
    writer.write(&tad3_bed).unwrap();
}
assert_eq!(
    "chrXII\t765265\t766358\tYLR316C\t0\t-\t765265\t766358\t0\t3\t808,52,109,\t0,864,984,\n",
    String::from_utf8(buf)
        .unwrap_or_else(|_| "???".to_owned())
        .as_str()
);

fn from(spliced: Spliced<R, S>) -> Self

Performs the conversion.

impl Serialize for Record

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.