This project follows the semver pro forma and uses the git-flow branching model.
This package provides read and write support for Bedgraph files.
Note: this package does not currently handle bedGraph meta data such as the track definition or browser lines.
You can install Bedgraph from the Julia REPL.
Press ] to enter pkg mode, then enter the following:
add BedgraphIf you are interested in the cutting edge of the development, please check out the develop branch to try new features before release.
See source for optional
bump_back,bump_forward, andright_openkey values. These options are included in the pertinent read/write functions to handle quirks of the zero-based and half-open nature of the bedGraph format.
using Bedgraph
header = read(file, BedgraphHeader{Vector{String}})Read all records at once.
using Bedgraph
records = read(file, Vector{Bedgraph.Record})using Bedgraph
records = open(file, "r") do io
return read(io, Vector{Bedgraph.Record})
endAlternatively you may want to read and process records individually.
open(file, "r") do io
while !eof(seek(io, Bedgraph.Record))
record = read(io, Bedgraph.Record) #Note: no protection.
# Process record.
end
endBedgraph.jl currently provides two write functions: one for Bedgraph.BedgraphHeader, and one for Bedgraph.Record, which also accepts Vector{Bedgraph.Record}.
using Bedgraph
const chroms = ["chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19"]
const firsts = [49302000, 49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400]
const lasts = [49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400, 49304700]
const values = [-1.0, -0.75, -0.50, -0.25, 0.0, 0.25, 0.50, 0.75, 1.00]
records = Bedgraph.Record.(chroms, firsts, lasts, values)
sort!(records)
header = Bedgraph.generate_basic_header(records)
write("data.bedgraph", header, records)using Bedgraph
records = [Record("chr19", 49302000, 49302300, -1.0), Record("chr19", 49302300, 49302600, -1.75)]
header = Bedgraph.generate_basic_header("chr19", records[1].first, records[end].last, bump_forward=false)
open(output_file, "w") do io
write(io, header, records)
endBelow are some examples of Bedgraph.Record conversions provided by this package.
using Bedgraph
record = Record("chr1", 10, 20)
# Convert record to NamedTuple.
nt = convert(NamedTuple, record)
# Convert record to NamedTuple and rename fields.
nt = convert(NamedTuple{(:chrom, :left, :right, :value)}, record)
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