Struct needletail::sequence_record::SequenceRecord

pub struct SequenceRecord<'a> {
    pub id: Cow<'a, [u8]>,
    pub seq: Cow<'a, [u8]>,
    pub qual: Option<Cow<'a, [u8]>>,
}

An intermediate structure for handling sequence data and harmonizing both FASTA and FASTQ records into a common format.

Fields

id: Cow<'a, [u8]>

seq: Cow<'a, [u8]>

qual: Option<Cow<'a, [u8]>>

Methods

impl<'a> SequenceRecord<'a>

pub fn new(
    id: Cow<'a, [u8]>,
    seq: Cow<'a, [u8]>,
    qual: Option<Cow<'a, [u8]>>
) -> Self

Creates a new SequenceRecord

pub fn mask_header(self) -> Self

Fixes up potential problems with sequence headers including tabs being present (may break downstream analyses with headers in TSVs) and with non-UTF8 characters being present, e.g. non-breaking spaces on Windows encodings (0x0A) breaks some tools.

pub fn write_fasta(
    &self,
    writer: &mut dyn Write,
    ending: &[u8]
) -> Result<(), ParseError>

Write this SequenceRecord to writer as a FASTA with the provided line ending (ending should be either \r\n or preferably \n).

pub fn write_fastq(
    &self,
    writer: &mut dyn Write,
    ending: &[u8]
) -> Result<(), ParseError>

Write this SequenceRecord to writer as a FASTQ with the provided line ending (ending should be either \r\n or preferably \n).

Trait Implementations

impl<'a> Sequence<'a> for SequenceRecord<'a>

fn sequence(&'a self) -> &'a [u8]

fn strip_returns(&'a self) -> Cow<'a, [u8]>

Remove newlines from the sequence; this handles \r, \n, and \r\n and removes internal newlines in addition to ones at the end. Primarily used for FASTA multiline records, but can also help process (the much rarer) multiline FASTQs. Always use before iteration methods below to ensure no newlines are being returned with e.g. .kmers.

fn reverse_complement(&'a self) -> Vec<u8>

Returns the reverse complement of a sequence. Biologically this is equivalent to the sequence of the strand opposite the one you pass in.

fn normalize(&'a self, iupac: bool) -> Cow<'a, [u8]>

[Nucleic Acids] Normalizes the sequence. See documentation for needletail::sequence::normalize. Do not use on amino acid sequences. Note that this returns a Cow so you may have to coerce to a Vec or &u8 as necessary.

Important traits for CanonicalKmers<'a>

impl<'a> Iterator for CanonicalKmers<'a> type Item = (usize, &'a [u8], bool);

fn canonical_kmers(
    &'a self,
    k: u8,
    reverse_complement: &'a [u8]
) -> CanonicalKmers<'a>

[Nucleic Acids] Returns an iterator over the sequence that skips non-ACGT bases and returns a tuple containing (position, the canonicalized kmer, if the sequence is the complement of the original).

Important traits for Kmers<'a>

impl<'a> Iterator for Kmers<'a> type Item = &'a [u8];

fn kmers(&'a self, k: u8) -> Kmers<'a>

Returns an iterator that returns a sliding window of k-sized sequences (k-mers). Does not skip whitespace or correct bases in the original sequence so .normalize or .strip_returns may be appropriate to use first.

Important traits for BitNuclKmer<'a>

impl<'a> Iterator for BitNuclKmer<'a> type Item = (usize, BitKmer, bool);

fn bit_kmers(&'a self, k: u8, canonical: bool) -> BitNuclKmer<'a>

Return an iterator that returns valid kmers in 4-bit form

impl<'a> QualitySequence<'a> for SequenceRecord<'a>

fn quality(&'a self) -> &'a [u8]

fn quality_mask(&'a self, score: u8) -> Cow<'a, [u8]>

Given a SeqRecord and a quality cutoff, mask out low-quality bases with N characters.

impl<'a> From<FastaRecord<'a>> for SequenceRecord<'a>

fn from(fasta: FastaRecord<'a>) -> SequenceRecord<'a>

Performs the conversion.

impl<'a> From<FastqRecord<'a>> for SequenceRecord<'a>

fn from(fastq: FastqRecord<'a>) -> SequenceRecord<'a>

Performs the conversion.

impl<'a> From<&'a [u8]> for SequenceRecord<'a>

fn from(slice: &'a [u8]) -> Self

Performs the conversion.