diff --git a/Project.toml b/Project.toml index e2bd1f8..c3f5004 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "BedgraphFiles" uuid = "85eb9095-274b-55ce-be28-9e90f41ac741" authors = ["Ciarán O'Mara "] -version = "2.1.1" +version = "2.1.2" [deps] Bedgraph = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd" @@ -15,19 +15,20 @@ TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda" [compat] -julia = "0.7, ^1" Bedgraph = "^1.1" FileIO = "^1.0.1" -IteratorInterfaceExtensions = "^0.1.1, ^1" IterableTables = ">=0.9.0" +IteratorInterfaceExtensions = "^0.1.1, ^1" TableShowUtils = "^0.2.0" TableTraits = "^0.4, ^1" TableTraitsUtils = "^0.3, ^0.4" +julia = "0.7, ^1" [extras] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Query = "1a8c2f83-1ff3-5112-b086-8aa67b057ba1" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" [targets] -test = ["DataFrames", "Test", "Query"] +test = ["DataFrames", "Test", "Query", "Logging"] diff --git a/README.md b/README.md index 13204e3..6c933ff 100644 --- a/README.md +++ b/README.md @@ -8,13 +8,11 @@ ## Overview -This package provides load and save support for [Bedgraph files](https://github.com/CiaranOMara/Bedgraph.jl) -under the [FileIO.jl](https://github.com/JuliaIO/FileIO.jl) package. - -This package is largely -- if not completely -- inspired by the work of [David Anthoff](https://github.com/davidanthoff). +This package provides load and save support for [Bedgraph](https://github.com/CiaranOMara/Bedgraph.jl) +under the [FileIO](https://github.com/JuliaIO/FileIO.jl) package, and also implements the [IterableTables](https://github.com/davidanthoff/IterableTables.jl) interface for easy conversion between tabular data structures. ## Installation -Install BedgraphFiles from the Julia REPL: +You can install BedgraphFiles from the Julia REPL: ```julia using Pkg add("BedgraphFiles") @@ -23,21 +21,20 @@ add("BedgraphFiles") ## Usage -### Loading a Bedgraph file - -To load a Bedgraph file into a ``Vector{Bedgraph.Record}``, use the following Julia code: +### Loading bedGraph files +To load a bedGraph file into a ``Vector{Bedgraph.Record}``, use the following Julia code: ````julia using FileIO, BedgraphFiles, Bedgraph records = Vector{Bedgraph.Record}(load("data.bedgraph")) ```` -### Saving a Bedgraph file +### Saving bedGraph files > **Note:** saving on top of an existing file will overwrite metadata/header information with a minimal working header. -The following example saves a ``Vector{Bedgraph.Record}`` to a Bedgraph file: +The following example saves a ``Vector{Bedgraph.Record}`` to a bedGraph file: ````julia using FileIO, BedgraphFiles, Bedgraph @@ -47,18 +44,16 @@ save("output.bedgraph", records) ```` ### IterableTables -The call to ``load`` returns a ``struct`` that is an [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl), so it can be passed to any function that can handle iterable tables, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl). - -To load a Bedgraph file into a `DataFrame`, use the following Julia code: +The execution of ``load`` returns a ``struct`` that adheres to the [IterableTables](https://github.com/davidanthoff/IterableTables.jl) interface, and can be passed to any function that also implements the interface, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl). +The following code shows an example of loading a bedGraph file into a [DataFrame](https://github.com/JuliaData/DataFrames.jl): ```julia using FileIO, BedgraphFiles, DataFrames df = DataFrame(load("data.bedgraph")) ``` -Here are some examples of materialising a Bedgraph file into data structures that are not a `DataFrame`: - +Here are some more examples of materialising a bedGraph file into other data structures: ```julia using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly @@ -69,10 +64,10 @@ dt = DataTable(load("data.bedgraph")) it = IndexedTable(load("data.bedgraph")) # Plot directly with Gadfly -plot(load("data.bedgraph"), x=:a, y=:b, Geom.line) +plot(load("data.bedgraph"), xmin=:leftposition, xmax=:rightposition, y=:value, Geom.bar) ``` -The following code saves any iterable table as a Bedgraph file: +The following code saves any compatible source to a bedGraph file: ```julia using FileIO, BedgraphFiles @@ -80,13 +75,10 @@ it = getiterator(data) save("output.bedgraph", it) ``` -This will work as long as `it` is any of the types supported as sources in [IterableTables.jl](https://github.com/davidanthoff/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: - +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: ```julia using FileIO, BedgraphFiles, DataFrame @@ -94,24 +86,23 @@ df = load("data.bedgraph") |> DataFrame ``` To save an iterable table, one can use the following form: - ```julia using FileIO, BedgraphFiles, DataFrame -df = # Aquire a DataFrame somehow +df = # Aquire a DataFrame somehow. df |> save("output.bedgraph") ``` The `save` method returns the data provided or `Vector{Bedgraph.Record}`. This is useful when periodically saving your work during a sequence of operations. - ```julia records = some sequence of operations |> save("output.bedgraph") ``` -The pipe syntax is especially useful when combining it with [Query.jl](https://github.com/davidanthoff/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. - +The pipe syntax is especially useful when combining it with [Query.jl](https://github.com/davidanthoff/Query.jl) queries. For example, one can easily load a bedGraph file, pipe its data into a query, and then store the query result by piping it to the `save` function. ```julia using FileIO, BedgraphFiles, Query load("data.bedgraph") |> @filter(_.chrom == "chr19") |> save("data-chr19.bedgraph") ``` +## Acknowledgements +This package is largely -- if not completely -- inspired by the work of [David Anthoff](https://github.com/davidanthoff). Other influences are from the [BioJulia](https://github.com/BioJulia) community.