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JSeqArray.jl Documentation

Functions

# JSeqArray.seqOpen — Function.

seqOpen(filename, readonly, allow_dup)

Opens a SeqArray GDS file.

Arguments

  • filename::String: the file name of a SeqArray file
  • readonly::Bool=true: if true, the file is opened read-only; otherwise, it is allowed to write data to the file
  • allow_dup::Bool=false: if true, it is allowed to open a GDS file with read-only mode when it has been opened in the same session

Examples

julia> f = seqOpen(seqExample(:kg))

julia> f

julia> seqClose(f)

# JSeqArray.seqClose — Method.

seqClose(file)

Closes a SeqArray GDS file which is open.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object

# JSeqArray.seqFilterSet — Method.

seqFilterSet(file; sample_id, variant_id, intersect, verbose)

Sets a filter to sample and/or variant.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • sample_id::Union{Void, Vector}=nothing: sample ID to be selected, or nothing for no action
  • variant_id::Union{Void, Vector}=nothing: variant ID to be selected, or nothing for no action
  • intersect::Bool=false: if false, the candidate samples/variants for selection are all samples/variants; if true, the candidate samples/variants are from the selected samples/variants defined via the previous call
  • verbose::Bool=true: if true, show information

Examples

julia> f = seqOpen(seqExample(:kg));

julia> sid = seqGetData(f, "sample.id");

julia> vid = seqGetData(f, "variant.id");

julia> seqFilterSet(f, sample_id=sid[4:10], variant_id=vid[2:6])
Number of selected samples: 7
Number of selected variants: 5

julia> seqClose(f)

# JSeqArray.seqFilterSet2 — Method.

seqFilterSet2(file; sample, variant, intersect, verbose)

Sets a filter to sample and/or variant.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • sample::Union{Void, Vector{Bool}, Vector{Int}, UnitRange{Int}}=nothing: sample(s) to be selected, or nothing for no action
  • variant::Union{Void, Vector{Bool}, Vector{Int}, UnitRange{Int}}=nothing: variant(s) to be selected, or nothing for no action
  • intersect::Bool=false: if false, the candidate samples/variants for selection are all samples/variants; if true, the candidate samples/variants are from the selected samples/variants defined via the previous call
  • verbose::Bool=true: if true, show information

Examples

julia> f = seqOpen(seqExample(:kg));

julia> seqFilterSet2(f, sample=4:10, variant=2:6)
Number of selected samples: 7
Number of selected variants: 5

julia> seqClose(f)

# JSeqArray.seqFilterSplit — Method.

seqFilterSplit(file, index, count; verbose)

Splits the variants into multiple parts equally and selects the specified part.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • index::Int: selects the indexth part (starting from 1)
  • index::Int: the total number of non-overlapping parts
  • verbose::Bool=true: if true, show information

Details

Users can define a subset of variants before calling seqFilterSplit() and split the selection of variants into multiple parts.

Examples

julia> f = seqOpen(seqExample(:kg));

julia> seqFilterSplit(f, 2, 5)
Number of selected variants: 3,954

julia> seqClose(f)

# JSeqArray.seqFilterReset — Method.

seqFilterReset(file; sample, variant, verbose)

Resets the sample and variant filters.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • sample::Bool=true: if true, resets the sample filter
  • variant::Bool=true: if true, resets the variant filter
  • verbose::Bool=true: if true, show information

# JSeqArray.seqFilterPush — Function.

seqFilterPush(file, reset)

Pushes the sample and variant filters to the stack for future uses.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • reset::Bool=false: if true, reset the sample and variant filters

# JSeqArray.seqFilterPop — Method.

seqFilterPop(file)

Uses the last sample and variant filters saved in the stack, and removes them from the stack.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object

# JSeqArray.seqFilterGet — Function.

seqFilterGet(file, sample)

Gets the filter of samples and variants.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • sample::Bool=true: if true, returns a logical vector for the sample filter; otherwise, returns a logical vector for the variant filter

# JSeqArray.seqGetData — Method.

seqGetData(file, name)

Gets data from a SeqArray GDS file.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • name::String: the variable name, see the details

Details

The variable name should be

  • "sample.id", "variant.id", "position", "chromosome", "allele"
  • "genotype" for 3-dim UInt8 array (ploidy, sample, variant) where 0 is the reference allele, 1 is the first alternative allele, 0xFF is missing value
  • "annotation/id", "annotation/qual", "annotation/filter", "annotation/info/VARIABLE_NAME", "annotation/format/VARIABLE_NAME"
  • "#dosage" for a dosage matrix (sample, variant) of reference allele (UInt8: 0, 1 and 2 for diploid genotypes, 0xFF for missing values)
  • "#num_allele" returns an integer vector with the numbers of distinct alleles

Examples

julia> f = seqOpen(seqExample(:kg));

julia> pos = seqGetData(f, "position"); println(typeof(pos), ", ", length(pos))
Array{Int32,1}, 19773

julia> geno = seqGetData(f, "genotype"); println(typeof(geno), ", ", size(geno))
Array{UInt8,3}, (2,1092,19773)

julia> dosage = seqGetData(f, "#dosage"); println(typeof(dosage), ", ", size(dosage))
Array{UInt8,2}, (1092,19773)

julia> seqClose(f)

# JSeqArray.seqApply — Method.

seqApply(fun, file, name, args...; asis, bsize, verbose, kwargs...)

Applies the user-defined function over array margins.

Arguments

  • fun::Function: the user-defined function
  • file::TSeqGDSFile: a SeqArray julia object
  • name::Union{String, Vector{String}}: the variable name(s), see the details
  • args: the optional arguments passed to the user-defined function
  • asis::Symbol=:none: :none (no return), :unlist (returns a vector which contains all the atomic components) or :list (returns a vector according to each block)
  • bsize::Int=1024: block size for the number of variants in a block
  • verbose::Bool=true: if true, show progress information
  • kwargs: the keyword optional arguments passed to the user-defined function

Details

The variable name should be

  • "sample.id", "variant.id", "position", "chromosome", "allele"
  • "genotype" for 3-dim UInt8 array (ploidy, sample, variant) where 0 is the reference allele, 1 is the first alternative allele, 0xFF is missing value
  • "annotation/id", "annotation/qual", "annotation/filter", "annotation/info/VARIABLE_NAME", "annotation/format/VARIABLE_NAME"
  • "#dosage" for a dosage matrix (sample, variant) of reference allele (UInt8: 0, 1 and 2 for diploid genotypes, 0xFF for missing values)
  • "#num_allele" returns an integer vector with the numbers of distinct alleles

The algorithm is highly optimized by blocking the computations to exploit the high-speed memory instead of disk.

Examples

julia> f = seqOpen(seqExample(:kg));

julia> s = seqApply(f, "genotype", asis=:unlist, verbose=false) do geno
           return sum(geno)
       end;

julia> Int(sum(s))
3083127

julia> seqClose(f)

# JSeqArray.seqParallel — Method.

seqParallel(fun, file, args...; split, combine, kwargs...)

Applies a user-defined function in parallel.

Arguments

  • fun::Function: the user-defined function
  • file::TSeqGDSFile: a SeqArray julia object
  • args: the optional arguments passed to the user-defined function
  • split::Symbol=:byvariant: :none for no split, :byvariant for spliting the dataset by variant according to multiple processes
  • combine::Union{Symbol, Function}=:unlist: :none (no return), :unlist (returns a vector which contains all the atomic components) or :list (returns a vector according to each process)
  • kwargs: the keyword optional arguments passed to the user-defined function

Details

Examples

# JSeqArray.seqAttr — Method.

seqAttr(file, name)

Applies a user-defined function in parallel.

Arguments

  • file::TSeqGDSFile: a SeqArray julia object
  • name::Symbol: the symbol name for a specified attribute

Details

name::Symbol =

  • :nsampe - the total number of samples
  • :nselsamp - the number of selected samples
  • :nvar - the total number of variants
  • :nselvar - the number of selected variants
  • :ploidy - the number of sets of chromosomes

Examples

julia> f = seqOpen(seqExample(:kg));

julia> seqFilterSet2(f, sample=5:10, variant=31:40)
Number of selected samples: 6
Number of selected variants: 10

julia> seqAttr(f, :nsamp)
1092

julia> seqAttr(f, :nselsamp)
6

julia> seqAttr(f, :nvar)
19773

julia> seqAttr(f, :nselvar)
10

julia> seqAttr(f, :ploidy)
2

julia> seqClose(f)

# JSeqArray.seqExample — Method.

seqExample(file)

Returns the example SeqArray file.

Arguments

  • file::Symbol: specify which SeqArray file, it should be :kg for 1KG_phase1_release_v3_chr22.gds

Examples

julia> fn = seqExample(:kg);

julia> basename(fn)
"1KG_phase1_release_v3_chr22.gds"

# Base.show — Method.

show(io, file; attr, all)

Applies a user-defined function in parallel.

Arguments

  • io::: I/O stream
  • file::TSeqGDSFile: a SeqArray julia object
  • attr::Bool=false: if true, shows all attributes
  • all::Bool=false: if true, show all GDS nodes including hidden nodes