https://github.com/ciaranomara/bedgraph.jl
Read and write support for bedGraph file format.
https://github.com/ciaranomara/bedgraph.jl
bedgraph bioinformatics dna julia
Last synced: about 1 year ago
JSON representation
Read and write support for bedGraph file format.
- Host: GitHub
- URL: https://github.com/ciaranomara/bedgraph.jl
- Owner: CiaranOMara
- License: mit
- Created: 2017-08-17T08:00:43.000Z (almost 9 years ago)
- Default Branch: develop
- Last Pushed: 2024-05-05T09:55:10.000Z (about 2 years ago)
- Last Synced: 2024-10-19T15:20:06.376Z (over 1 year ago)
- Topics: bedgraph, bioinformatics, dna, julia
- Language: Julia
- Homepage:
- Size: 126 KB
- Stars: 0
- Watchers: 1
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Bedgraph.jl
[](http://www.repostatus.org/#wip)
[](https://codecov.io/gh/CiaranOMara/Bedgraph.jl?branch=master)
> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](http://nvie.com/git-model "original
blog post").
## Description
This package provides read and write support for [Bedgraph files](https://genome.ucsc.edu/goldenPath/help/bedgraph.html).
> **Note:** this package does not currently handle bedGraph meta data such as the track definition or browser lines.
## Installation
You can install Bedgraph from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following:
```julia
add Bedgraph
```
If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/CiaranOMara/Bedgraph.jl/tree/develop) to try new features before release.
## Usage
### Reading and writing bedGraph files
> See source for optional `bump_back`, `bump_forward`, and `right_open` key 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.
#### Read header/meta
```julia
using Bedgraph
header = read(file, BedgraphHeader{Vector{String}})
```
#### Read records
Read all records at once.
```julia
using Bedgraph
records = read(file, Vector{Bedgraph.Record})
```
```julia
using Bedgraph
records = open(file, "r") do io
return read(io, Vector{Bedgraph.Record})
end
```
Alternatively you may want to read and process records individually.
```julia
open(file, "r") do io
while !eof(seek(io, Bedgraph.Record))
record = read(io, Bedgraph.Record) #Note: no protection.
# Process record.
end
end
```
#### Write a bedGraph file
Bedgraph.jl currently provides two write functions: one for `Bedgraph.BedgraphHeader`, and one for `Bedgraph.Record`, which also accepts `Vector{Bedgraph.Record}`.
```julia
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)
```
```julia
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)
end
```
#### Converting records
Below are some examples of `Bedgraph.Record` conversions provided by this package.
```julia
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)
```