Struct twobit::TwoBitFile

pub struct TwoBitFile { /* fields omitted */ }

Read data from a 2bit file

Usage:

extern crate twobit;
use twobit::TwoBitFile;

let enable_softmask=true; //set to false to enforce upper case sequences
let tb = TwoBitFile::open("assets/foo.2bit", enable_softmask).unwrap();
let chromosome_lengths = tb.chroms();
assert_eq!(chromosome_lengths["chr1"], 150);
assert_eq!(chromosome_lengths["chr2"], 100);

2bit files offer two types of masks: N masks (aka hard masks) for unknown or arbitrary nucleotides and soft masks for lower-case nucleotides (e.g. "t" instead of "T").

let expected_seq = "NNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATC"; // some lower and some upper case
assert_eq!(tb.sequence("chr1",24,74).unwrap(), expected_seq);

It is not possible to disable hard masks but you can disable soft masks:

let enable_softmask=false;
let tb_nosoft = TwoBitFile::open("assets/foo.2bit", enable_softmask).unwrap();
let expected_seq = "NNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTAGCTAGCTGATC"; // all upper case
assert_eq!(tb_nosoft.sequence("chr1",24,74).unwrap(), expected_seq);

There are 2 variants for every sequence-related method:

• Those that request information on parts of a chromosome
• Those that request information on a complete chromosome

The partial requests require you to provide a start (0-based, inclusive) and a stop (0-based, exclusive) position as parameters. The full request methods all start with the prefix full_.

Implementations

impl TwoBitFile

pub fn open<P: AsRef<Path>>(
    path: P,
    softmask_enabled: bool
) -> Result<TwoBitFile, Error>

Constructor for a 2bit file.

• path - A path to the 2bit file
• softmask_enabled - return lower case nucleotides for soft blocks

pub fn chroms(&self) -> HashMap<String, Field>

Get the sizes of chromosomes in a 2bit file as a HashMap

pub fn full_sequence(&self, chr: &str) -> Result<String, Error>

Get the full sequence of a chromosome

• chr Name of the chromosome from the 2bit file
• returns the full sequence as a String on success

pub fn sequence(
    &self,
    chr: &str,
    start: usize,
    end: usize
) -> Result<String, Error>

Get a partial sequence of a chromosome

• chr Name of the chromosome from the 2bit file
• start Start position of the sequence
• end Stop position of the sequence
• returns the full sequence as a String on success

pub fn full_bases(&self, chr: &str) -> Result<BaseCounts, Error>

Count bases of a chromosome

• chr Name of the chromosome from the 2bit file

pub fn full_bases_percentages(
    &self,
    chr: &str
) -> Result<BasePercentages, Error>

Calculates percentages of bases of a chromosome

• chr Name of the chromosome from the 2bit file

pub fn bases(
    &self,
    chr: &str,
    start: usize,
    end: usize
) -> Result<BaseCounts, Error>

Count bases of a partial chromosome

• chr Name of the chromosome from the 2bit file

pub fn bases_percentages(
    &self,
    chr: &str,
    start: usize,
    end: usize
) -> Result<BasePercentages, Error>

Calculates percentages of bases of a partial chromosome

• chr Name of the chromosome from the 2bit file

pub fn info(&self) -> Result<TwoBitFileInfo, Error>

Obtain general information on the 2bit file you are dealing with

pub fn full_hard_masked_blocks(&self, chr: &str) -> Result<Vec<Block>, Error>

Get all hard blocks (N-blocks) of a chromosome

• chr Name of the chromosome from the 2bit file

pub fn hard_masked_blocks(
    &self,
    chr: &str,
    start: usize,
    end: usize
) -> Result<Vec<Block>, Error>

Get hard blocks (N-blocks) of a region on a chromosome

• chr Name of the chromosome from the 2bit file

pub fn full_soft_masked_blocks(&self, chr: &str) -> Result<Vec<Block>, Error>

Get all soft blocks (lower case blocks) of a chromosome

• chr Name of the chromosome from the 2bit file

pub fn soft_masked_blocks(
    &self,
    chr: &str,
    start: usize,
    end: usize
) -> Result<Vec<Block>, Error>

Get soft blocks (lower case blocks) of a region on a chromosome

• chr Name of the chromosome from the 2bit file