Struct atglib::spliceai::Writer

pub struct Writer<W: Write> { /* private fields */ }

Writes Transcripts into a BufWriter to be used as gene annotation by SpliceAI

Examples

use atglib::tests;;
use atglib::spliceai::Writer;
use atglib::models::TranscriptWrite;

let transcripts = vec![tests::transcripts::standard_transcript()];

let output = Vec::new(); // substitute this with proper IO (io::stdout())
let mut writer = Writer::new(output);
writer.write_transcript_vec(&transcripts);

assert_eq!(
writer.into_inner().unwrap(), // this is our actual output
b"#NAME\tCHROM\tSTRAND\tTX_START\tTX_END\tEXON_START\tEXON_END
Test-Gene\tchr1\t+\t11\t55\t11,21,31,41,51,\t15,25,35,45,55,
"
);

Implementations

impl Writer<File>

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

impl<W: Write> Writer<W>

pub fn new(writer: W) -> Self

Creates a new generic Writer for any `std::io::Read`` object

Use this method when you want to write to stdout or a remote source, e.g. via HTTP

pub fn with_capacity(capacity: usize, writer: W) -> Self

pub fn flush(&mut self) -> Result<(), AtgError>

pub fn into_inner(self) -> Result<W, AtgError>

pub fn write_header(&mut self) -> Result<(), Error>

Trait Implementations

impl<W: Write> TranscriptWrite for Writer<W>

fn writeln_single_transcript( &mut self, transcript: &Transcript ) -> Result<(), Error>

Writes a single transcript formatted for SpliceAI with an extra newline

fn write_single_transcript( &mut self, transcript: &Transcript ) -> Result<(), Error>

fn write_transcripts(&mut self, transcripts: &Transcripts) -> Result<(), Error>

fn write_transcript_vec( &mut self, transcripts: &[Transcript] ) -> Result<(), Error>