FileIO.jl integration for bedGraph files
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README.md

BedgraphFiles.jl

Project Status: Active - The project has reached a stable, usable state and is being actively developed. Build Status Build status BedgraphFiles codecov.io Coverage Status

Overview

This package provides load and save support for Bedgraph files under the FileIO.jl package.

This package is largely -- if not completely -- inspired by the work of David Anthoff.

Installation

Use Pkg.add("BedgraphFiles") in Julia to install BedgraphFiles and its dependencies.

Usage

Load a Bedgraph file

To read a Bedgraph file into a DataFrame, use the following Julia code:

using FileIO, BedgraphFiles, DataFrames

df = DataFrame(load("data.bedgraph"))

The call to load returns a struct that is an IterableTable.jl, so it can be passed to any function that can handle iterable tables, i.e. all the sinks in IterableTable.jl. Here are some examples of materialising a Bedgraph file into data structures that are not a DataFrame:

using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly

# Load into a DataTable
dt = DataTable(load("data.bedgraph"))

# Load into an IndexedTable
it = IndexedTable(load("data.bedgraph"))

# Plot directly with Gadfly
plot(load("data.bedgraph"), x=:a, y=:b, Geom.line)

Save a Bedgraph file

Note: saving on top of an existing file will overwrite metadata/header information with a minimal working header.

The following code saves any iterable table as a Bedgraph file:

using FileIO, BedgraphFiles

save("output.bedgraph", it)

This will work as long as it is any of the types supported as sources in IterableTables.jl.

Using the pipe syntax

Both load and save also support the pipe syntax. For example, to load a Bedgraph file into a DataFrame, one can use the following code:

using FileIO, BedgraphFiles, DataFrame

df = load("data.bedgraph") |> DataFrame

To save an iterable table, one can use the following form:

using FileIO, BedgraphFiles, DataFrame

df = # Aquire a DataFrame somehow

df |> save("output.bedgraph")

The pipe syntax is especially useful when combining it with Query.jl queries, for example one can easily load a Bedgraph file, pipe it into a query, then pipe it to the save function to store the results in a new file.