Struct Reader

pub struct Reader<R> { /* private fields */ }

Parses RefGene data and creates Transcripts.

RefGene data can be read from a file, stdin or remote sources All sources are supported that provide a std::io::Read implementation.

Examples

use atglib::refgene::Reader;
use atglib::models::TranscriptRead;

// create a reader from the tests RefGene file
let reader = Reader::from_file("tests/data/example.refgene");
assert_eq!(reader.is_ok(), true);

// parse the RefGene file
let transcripts = reader
    .unwrap()
    .transcripts()
    .unwrap();

assert_eq!(transcripts.len(), 27);

Implementations

impl Reader<File>

pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self, ReadWriteError>

Creates a Reader instance that reads from a File

Use this method when you want to read from a RefGene file on your local file system

Examples

use atglib::refgene::Reader;
use atglib::models::TranscriptRead;

// create a reader from the tests RefGene file
let reader = Reader::from_file("tests/data/example.refgene");
assert_eq!(reader.is_ok(), true);

// parse the RefGene file
let transcripts = reader
    .unwrap()
    .transcripts()
    .unwrap();

assert_eq!(transcripts.len(), 27);

impl<R: Read> Reader<R>

pub fn new(reader: R) -> Self

creates a new Reader instance from any std::io::Read object

Use this method when you want to read from stdin or from a remote source, e.g. via HTTP

pub fn with_capacity(capacity: usize, reader: R) -> Self

Creates a new Reader instance with a known capcity

Use this when you know the size of your RefGene source

pub fn line(&mut self) -> Option<Result<Transcript, ParseRefGeneError>>

Returns one line of a RefGene file as Transcript

This method should rarely be used. GTF files can contain unordered records and handling lines individually is rarely desired.

Trait Implementations

impl<R: Read> TranscriptRead for Reader<R>

fn transcripts(&mut self) -> Result<Transcripts, ReadWriteError>

Reads in RefGene data and returns the final list of Transcripts

Examples

use atglib::refgene::Reader;
use atglib::models::TranscriptRead;

// create a reader from the tests RefGene file
let reader = Reader::from_file("tests/data/example.refgene");
assert_eq!(reader.is_ok(), true);

// parse the RefGene file
let transcripts = reader
    .unwrap()
    .transcripts()
    .unwrap();

assert_eq!(transcripts.len(), 27);