IO - 2bit formatted files

2bit is a binary file format designed for storing a genome consists of multiple chromosomal sequences. The reading speed is often an order of magnitude faster than that of FASTA and the file size is smaller. However, since the .2bit file format is specialized for genomic sequences, it cannot store either RNA or amino acid sequences.

Readers and Writers

The reader and writer for 2bit formatted files, are found within the BioSequences.TwoBit module.

BioSequences.TwoBit.Reader — Type.

TwoBit.Reader(input::IO)

Create a data reader of the 2bit file format.

Arguments

input: data source

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BioSequences.TwoBit.Writer — Type.

TwoBitWriter(output::IO, names::AbstractVector)

Create a data writer of the 2bit file format.

Arguments

output: data sink
names: a vector of sequence names written to output

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The 2bit reader supports random access using an index included in the header section of a .2bit file:

reader = TwoBit.Reader(open("sacCer.2bit", "r"))
chrIV = reader["chrIV"] # directly read chromosome 4

If you want to know the names of the sequences available in the file, you can use the seqnames method on the reader.

seqnames(reader)

Reading from a TwoBit.Reader will yield a TwoBit.Record type variable:

BioSequences.TwoBit.Record — Type.

TwoBit.Record()

Create an unfilled 2bit record.

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Record(name::AbstractString, seq::BioSequences.Sequence, masks::Union{Vector{UnitRange{Int}}, Nothing} = nothing)

Prepare a record for writing to a 2bit formatted file.

Needs a name, a sequence, and (optionally) masks: a vector of ranges that delineate masked regions of sequence.

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To write a sequence to a TwoBit file, first a record must be created.

BioSequences.TwoBit.Record — Method.

Record(name::AbstractString, seq::BioSequences.Sequence, masks::Union{Vector{UnitRange{Int}}, Nothing} = nothing)

Prepare a record for writing to a 2bit formatted file.

Needs a name, a sequence, and (optionally) masks: a vector of ranges that delineate masked regions of sequence.

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