Struct Writer

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pub struct Writer<W: Write, R: Read + Seek> { /* private fields */ }

Expand description

Writes QcChecks into a BufWriter

§Examples

use std::io;
use atglib::tests;;
use atglib::qc::Writer;
use atglib::fasta::FastaReader;
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.fasta_reader(FastaReader::from_file("tests/data/small.fasta").unwrap());
writer.write_transcript_vec(&transcripts);

let written_output = String::from_utf8(writer.into_inner().unwrap()).unwrap();
assert_eq!(written_output, "Test-Gene\tTest-Transcript\tOK\tNOK\tOK\tOK\tOK\tOK\tOK\n");

Implementations§

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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

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

Constructs a new, empty Writer with the specified capacity.

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pub fn fasta_reader(&mut self, r: FastaReader<R>)

Specify a [FastaReader'](crate::fasta::FastaReader`) to retrieve the reference genome sequence.

You must set a fasta_reader, since the Writer does not have any information about the reference genome to use.

use atglib::qc::Writer;
use atglib::fasta::FastaReader;

let output = Vec::new(); // substitute this with proper IO (io::stdout())
let mut writer = Writer::new(output);
// specify the reference genome fasta file
writer.fasta_reader(FastaReader::from_file("tests/data/small.fasta").unwrap());

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pub fn default_genetic_code(&mut self, code: GeneticCode)

Changes the default genetic code to a custom one

By default, the standard genetic code is used for translating to AminoAcids

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pub fn add_genetic_code(&mut self, chrom: String, code: GeneticCode)

Add a custom genetic code that will be used for all transcripts on chrom

For example, when using QC for human genomes, you should specify to use the vertebrate_mitochondria genetic code for all transcripts on the mitochondrial chromsome.

§Examples

use atglib::qc::Writer;
use atglib::fasta::FastaReader;
use atglib::models::GeneticCode;

let output = Vec::new(); // substitute this with proper IO (io::stdout())
let mut writer = Writer::new(output);
// specify the reference genome fasta file
writer.fasta_reader(FastaReader::from_file("tests/data/small.fasta").unwrap());
// use vertebrate_mitochondria genetic code for chrM transcripts
writer.add_genetic_code("chrM".to_string(), GeneticCode::vertebrate_mitochondrial());

let codes = writer.genetic_codes();
assert_eq!(codes[0].0, "*");
assert_eq!(codes[1].0, "chrM");

// The mitochondrial genetic code contains 4 Stop codons, the standard genetic code has 3:
assert_eq!(codes[0].1.stop_codons().len(), 3);
assert_eq!(codes[1].1.stop_codons().len(), 4);

§Note

The matching of chromosomes to genetic codes is implemented for use-cases with a maximum of 1 or 2 additional genetic codes. If you have use-cases where you need many different genetic codes it would be better to split your Transcripts beforehand.

It is optimized for vertebrate genomes (i.e. standard code + vertebrate mitochondrial code)

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