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Add switch to convert partial ambiguities into N #8

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cd99d02
Add to docs too
BioTurboNick Jun 30, 2025
6434765
Add switch to allow partial ambiguity to be processed
BioTurboNick Jun 30, 2025
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2 changes: 1 addition & 1 deletion docs/src/index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@

TwoBit.jl provides I/O and utilities for manipulating 2Bit sequence data files.

2Bit is a binary file format designed for storing a genome consists of multiple chromosomal sequences.
2Bit is a binary file format (described [here](https://genome.ucsc.edu/FAQ/FAQformat.html#format7)) designed for storing a genome that 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.

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16 changes: 9 additions & 7 deletions src/writer.jl
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Expand Up @@ -11,13 +11,15 @@ mutable struct Writer{T<:IO} <: BioGenerics.IO.AbstractWriter
end

"""
TwoBitWriter(output::IO, names::AbstractVector)
TwoBitWriter(output::IO, names::AbstractVector; collapse_ambiguous = false)

Create a data writer of the 2bit file format.

# Arguments
* `output`: data sink
* `names`: a vector of sequence names written to `output`
* `collapse_ambiguous`: Set to `true` if your input sequence has partial ambiguities (W/S/R/Y, etc.) and you can
tolerate converting them to `N`. The format does not support partial ambiguities and will error otherwise.
"""
function Writer(output::IO, names::AbstractVector)
writer = Writer(output, names, falses(length(names)))
Expand Down Expand Up @@ -73,7 +75,7 @@ function update_offset(writer::Writer, seqname, seqoffset)
end
end

function Base.write(writer::Writer, record::WriteRecord)
function Base.write(writer::Writer, record::WriteRecord; collapse_ambiguous = false)
i = findfirst(isequal(record.name), writer.names)
if i == 0
error("sequence \"", record.name, "\" doesn't exist in the writing list")
Expand All @@ -86,7 +88,7 @@ function Base.write(writer::Writer, record::WriteRecord)

n = 0
n += write(output, UInt32(length(record.seq)))
n += write_n_blocks(output, record.seq)
n += write_n_blocks(output, record.seq; collapse_ambiguous)
n += write_masked_blocks(output, record.masks)
n += write(output, UInt32(0)) # reserved bytes
n += write_twobit_sequence(output, record.seq)
Expand All @@ -95,13 +97,13 @@ function Base.write(writer::Writer, record::WriteRecord)
return n
end

function make_n_blocks(seq)
function make_n_blocks(seq; collapse_ambiguous = false)
starts = UInt32[]
sizes = UInt32[]
i = 1
while i ≤ lastindex(seq)
nt = seq[i]
if nt == BioSequences.DNA_N
if nt == BioSequences.DNA_N || (collapse_ambiguous && BioSequences.isambiguous(nt))
start = i - 1 # 0-based index
push!(starts, start)
while i ≤ lastindex(seq) && seq[i] == BioSequences.DNA_N
Expand All @@ -117,8 +119,8 @@ function make_n_blocks(seq)
return starts, sizes
end

function write_n_blocks(output, seq)
blockstarts, blocksizes = make_n_blocks(seq)
function write_n_blocks(output, seq; collapse_ambiguous = false)
blockstarts, blocksizes = make_n_blocks(seq; collapse_ambiguous)
@assert length(blockstarts) == length(blocksizes)
n = 0
n += write(output, UInt32(length(blockstarts)))
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