Struct Transcripts

pub struct Transcripts { /* private fields */ }

A convinience wrapper to handle large amounts of Transcripts

It allows fast lookup operation by gene or transcript name.

Examples

use atglib::models::{TranscriptBuilder, Transcripts};

let mut transcripts = Transcripts::new();
assert_eq!(transcripts.len(), 0);

transcripts.push(TranscriptBuilder::new()
    .name("NM_001203247.2")
    .chrom("chr7")
    .gene("EZH2")
    .strand(atglib::models::Strand::Minus)
    .build()
    .unwrap()
);
assert_eq!(transcripts.len(), 1);

assert_eq!(transcripts.by_name("NM_001203247.2").len(), 1);
assert_eq!(transcripts.by_gene("EZH2").len(), 1);

assert!(transcripts.by_name("Foo").is_empty());
assert!(transcripts.by_gene("Bar").is_empty());

Implementations

impl Transcripts

pub fn new() -> Self

pub fn with_capacity(capacity: usize) -> Self

pub fn by_name(&self, name: &str) -> Vec<&Transcript>

Retrieve all Transcripts by their name / transcript-id

Most transcripts exist only once, but some transcripts (e.g. NM_001370371.1) are on both X- and Y-chromosome.

Examples

assert_eq!(transcripts.by_name("NM_001203247.2").len(), 1);
assert!(transcripts.by_name("invalid_name").is_empty());

pub fn by_gene(&self, gene: &str) -> Vec<&Transcript>

Retrieve all Transcripts of a gene

Examples

assert_eq!(transcripts.by_gene("EZH2").len(), 1);
assert!(transcripts.by_gene("Invalid-name").is_empty());

pub fn push(&mut self, record: Transcript)

Add another Transcript

Examples

use atglib::models::{TranscriptBuilder, Transcripts};

let mut transcripts = Transcripts::new();

transcripts.push(TranscriptBuilder::new()
    .name("NM_001203247.2")
    .chrom("chr7")
    .gene("EZH2")
    .strand(atglib::models::Strand::Minus)
    .build()
    .unwrap()
);

transcripts.push(TranscriptBuilder::new()
    .name("NM_001203247.3")
    .chrom("chr7")
    .gene("EZH2")
    .strand(atglib::models::Strand::Minus)
    .build()
    .unwrap()
);
assert_eq!(transcripts.len(), 2);

assert_eq!(transcripts.by_name("NM_001203247.2").len(), 1);
assert_eq!(transcripts.by_name("NM_001203247.3").len(), 1);
assert_eq!(transcripts.by_gene("EZH2").len(), 2);

pub fn len(&self) -> usize

Returns the number of Transcripts in the object

pub fn is_empty(&self) -> bool

Returns true if the object contains no transcripts.

pub fn as_vec(&self) -> &Vec<Transcript>

Returns a vector of Transcripts

pub fn to_vec(self) -> Vec<Transcript>

Consumes and returns a vector of Transcripts

pub fn genes(&self) -> Vec<&str>

Returns a vector with the gene symbols of all transcripts

Trait Implementations

impl Default for Transcripts

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for Transcripts

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl IntoIterator for Transcripts

type Item = Transcript

The type of the elements being iterated over.

type IntoIter = IntoIter<<Transcripts as IntoIterator>::Item>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl Serialize for Transcripts

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

where __S: Serializer,

Serialize this value into the given Serde serializer.