Records

FASTX files are considered a sequence of Records, FASTA.Record for FASTA files and FASTQ.Record for FASTQ. For convenience, FASTARecord and FASTQRecord are aliases of FASTA.Record and FASTQ.Record.

A Record object represent the text of the FASTX record as it is, e.g the following FASTA record:

>some header here
TAGATGAA
AA

Is stored in a FASTA.Record object roughly as its constituent bytes, plus some metadata. There is no notion in the record object of being a DNA or RNA sequence - it's simply an array of bytes.

Records can be constructed from raw parts (i.e. description and sequence and, for FASTQ, quality), where

• description::AbstractString
• sequence::Union{AbstractString, BioSequence}
• quality::Union{AbstractString, Vector{<:Number}}

Alternatively, they can be parsed directly from a string or an AbstractVector{UInt8}.

julia> record = parse(FASTARecord, ">abc\nAGCC\nCCGA");

julia> record2 = FASTARecord("abc", "AGCCCCGA");

julia> record == record2
true

Records can be queried for their information, namely identifier, description and sequence (and quality, for FASTQ). By default, this returns an AbstractString view into the Record's data:

julia> record = parse(FASTARecord, ">ident desc\nUGU\nGA");

julia> (identifier(record), description(record), sequence(record))
("ident", "ident desc", "UGUGA")

However, you can ask for getting the sequences as a String or any subtype of BioSequence:

julia> record = parse(FASTARecord, ">abc\nUGC\nCCA");

julia> using BioSequences # LongRNA defined in BioSequences.jl

julia> sequence(LongRNA{2}, record)
6nt RNA Sequence:
UGCCCA

julia> sequence(String, record)
"UGCCCA"

The number of bytes in the sequence of a Record can be queried using seqsize:

julia> record = parse(FASTARecord, ">abc\nUGC\nCCA");

julia> seqsize(record)
6

Reference:

identifier(record::Record)::AbstractString

julia> record = parse(FASTA.Record, ">ident_here some descr \nTAGA");

julia> identifier(record)
"ident_here"

description(record::Record)::AbstractString

julia> record = parse(FASTA.Record, ">ident_here some descr \nTAGA");

julia> description(record)
"ident_here some descr "

sequence([::Type{S}], record::Record, [part::UnitRange{Int}])::S

julia> record = parse(FASTQ.Record, "@read1\nTAGA\n+\n;;]]");

julia> sequence(record)
"TAGA"

julia> sequence(LongDNA{2}, record)
4nt DNA Sequence:
TAGA

seqsize(::Record)::Int

julia> seqsize(parse(FASTA.Record, ">hdr\nKRRLPW\nYHS"))
9

julia> seqsize(parse(FASTA.Record, ">hdr\nαβγδϵ"))
10