Merge branch 'release/v2.1.0'

Manifest.toml

@@ -1,11 +1,13 @@
+# This file is machine-generated - editing it directly is not advised
+
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[Bedgraph]]
 deps = ["Test"]
-git-tree-sha1 = "815a4d7dad0145bb4560d77840d77b33e07861fe"
+git-tree-sha1 = "039106453269e691fb54fb14e2b40f6c26091f62"
 uuid = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
-version = "1.0.3"
+version = "1.1.0"
 
 [[BinaryProvider]]
 deps = ["Libdl", "Pkg", "SHA", "Test"]
@@ -64,7 +66,7 @@ deps = ["Mmap"]
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 
 [[Distributed]]
-deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
+deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[FileIO]]
@@ -78,7 +80,7 @@ deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[InteractiveUtils]]
-deps = ["LinearAlgebra", "Markdown"]
+deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[IterableTables]]
@@ -188,15 +190,15 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [[StatsBase]]
 deps = ["DataStructures", "DelimitedFiles", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "Test"]
-git-tree-sha1 = "7b596062316c7d846b67bf625d5963a832528598"
+git-tree-sha1 = "6479f15167b434c765d3508524264bfd63ded7c8"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.27.0"
+version = "0.28.0"
 
 [[TableShowUtils]]
 deps = ["DataValues", "Dates", "JSON", "Markdown", "Test"]
-git-tree-sha1 = "b588b0bc89c107e6598b2bac967205932634d92d"
+git-tree-sha1 = "14c54e1e96431fb87f0d2f5983f090f1b9d06457"
 uuid = "5e66a065-1f0a-5976-b372-e0b8c017ca10"
-version = "0.2.3"
+version = "0.2.5"
 
 [[TableTraits]]
 deps = ["IteratorInterfaceExtensions", "Test"]
@@ -206,15 +208,15 @@ version = "0.4.1"
 
 [[TableTraitsUtils]]
 deps = ["DataValues", "IteratorInterfaceExtensions", "Missings", "TableTraits", "Test"]
-git-tree-sha1 = "a355f1882d64881a11f853e64dcc353975c4df6e"
+git-tree-sha1 = "55133a5476b61ec31060e555ffe12da27ac13682"
 uuid = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
-version = "0.3.1"
+version = "0.4.0"
 
 [[Tables]]
 deps = ["IteratorInterfaceExtensions", "LinearAlgebra", "Requires", "TableTraits", "Test"]
-git-tree-sha1 = "37be2ed169d5771c1ac8d516d3bcb0093c49966e"
+git-tree-sha1 = "5aa45584645393c1717e0cc1f0362c2ea81470a9"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "0.1.15"
+version = "0.1.17"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
@@ -227,14 +229,14 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.8.1"
 
 [[UUIDs]]
-deps = ["Random"]
+deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[WeakRefStrings]]
 deps = ["Missings", "Random", "Test"]
-git-tree-sha1 = "bccf012a0e8815410ad8b6846944a33903992fc3"
+git-tree-sha1 = "cf70c71939e621a3fac4156a8bfb3c80d745794a"
 uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
-version = "0.5.6"
+version = "0.5.7"

Project.toml

@@ -1,7 +1,7 @@
 name = "BedgraphFiles"
 uuid = "85eb9095-274b-55ce-be28-9e90f41ac741"
 authors = ["Ciarán O'Mara <[email protected]>"]
-version = "2.0.2"
+version = "2.1.0"
 
 [deps]
 Bedgraph = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
@@ -14,8 +14,12 @@ TableShowUtils = "5e66a065-1f0a-5976-b372-e0b8c017ca10"
 TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
 
+[compat]
+Bedgraph = "^1.1"
+
 [extras]
+Query = "1a8c2f83-1ff3-5112-b086-8aa67b057ba1"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Query"]

README.md

@@ -24,19 +24,43 @@ add("BedgraphFiles")
 
 ## Usage
 
-### Load a Bedgraph file
+### Loading a Bedgraph file
 
-To read a Bedgraph file into a ``DataFrame``, use the following Julia code:
+To load a Bedgraph file into a ``Vector{Bedgraph.Record}``, use the following Julia code:
 
 ````julia
-using FileIO, BedgraphFiles, DataFrames
+using FileIO, BedgraphFiles, Bedgraph
 
-df = DataFrame(load("data.bedgraph"))
+records = Vector{Bedgraph.Record}(load("data.bedgraph"))
 ````
 
-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). Here are some examples of materialising a Bedgraph file into data structures that are not a ``DataFrame``:
+### Saving a Bedgraph file
+
+> **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:
 ````julia
+using FileIO, BedgraphFiles, Bedgraph
+
+records = [Bedgraph.Record("chr", i, i + 99, rand()) for i in 1:100:1000]
+
+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:
+
+```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`:
+
+```julia
 using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly
 
 # Load into a DataTable
@@ -47,38 +71,48 @@ 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:
-````julia
+```julia
 using FileIO, BedgraphFiles
 
+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).
+```
+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
+```julia
 using FileIO, BedgraphFiles, DataFrame
 
 df = load("data.bedgraph") |> DataFrame
-````
+```
 
 To save an iterable table, one can use the following form:
 
-````julia
+```julia
 using FileIO, BedgraphFiles, DataFrame
 
 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.
 
-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.
+```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.
+
+```julia
+using FileIO, BedgraphFiles, Query
+load("data.bedgraph") |> @filter(_.chrom == "chr19") |> save("data-chr19.bedgraph")
+```

REQUIRE

@@ -1,5 +1,5 @@
 julia 0.7
-Bedgraph 1.0.0
+Bedgraph 1.1.0
 DataFrames 0.9.0
 FileIO 1.0.1
 IterableTables 0.9.0

src/BedgraphFiles.jl

@@ -19,6 +19,21 @@ struct BedgraphFile
     keywords
 end
 
+function Base.convert(::Type{Bedgraph.Record}, row::DataFrameRow) :: Bedgraph.Record
+    return Bedgraph.Record(row[1], row[2], row[3], row[4]) # Note: using index to allow flexible column names.
+end
+
+function Base.convert(::Type{Vector{Bedgraph.Record}}, df::DataFrame) :: Vector{Bedgraph.Record}
+
+    records = Vector{Bedgraph.Record}(undef, size(df)[1])
+
+    for (i, row) in enumerate(eachrow(df))
+        records[i] = convert(Bedgraph.Record, row)
+    end
+
+    return records
+end
+
 function Base.show(io::IO, source::BedgraphFile)
     TableShowUtils.printtable(io, getiterator(source), "bedGraph file")
 end
@@ -29,27 +44,38 @@ end
 
 IteratorInterfaceExtensions.isiterable(x::BedgraphFile) = true
 TableTraits.isiterabletable(x::BedgraphFile) = true
+IteratorInterfaceExtensions.isiterable(x::Vector{Bedgraph.Record}) = true #Note: Vector{Bedgraph.Record} is iterable by default.
+TableTraits.isiterabletable(x::Vector{Bedgraph.Record}) = true
 
-function _loaddata(path)
+
+function _loaddata(path) :: Vector{Bedgraph.Record}
     # Read file using bedgraph package.
     return open(path, "r") do io
         Bedgraph.readRecords(io)
     end
 end
 
+function IteratorInterfaceExtensions.getiterator(records::Vector{Bedgraph.Record})
+
+    columns = [
+        Bedgraph.chrom.(records),
+        Bedgraph.first.(records),
+        Bedgraph.last.(records),
+        Bedgraph.value.(records)
+    ]
+
+    names = Symbol[:chrom, :first, :last, :value]
+
+    it = TableTraitsUtils.create_tableiterator(columns, names)
+
+    return it
+end
+
 function IteratorInterfaceExtensions.getiterator(file::BedgraphFile)
 
     records = _loaddata(file.filename)
 
-    # Pack records into DataFrame.
-    df = DataFrame(
-        chrom = Bedgraph.chrom.(records)::Vector{String},
-        first = first.(records)::Vector{Int},
-        last = last.(records)::Vector{Int},
-        value = Bedgraph.value.(records)
-    )
-
-    it = getiterator(df)
+    it = getiterator(records)
 
     return it
 end
@@ -58,36 +84,58 @@ function Base.collect(x::BedgraphFile)
     return collect(getiterator(x))
 end
 
-function save(file::BedgraphFileFormat, header::Bedgraph.BedgraphHeader, records::Vector{Bedgraph.Record})
+function _Records(x) :: Vector{Bedgraph.Record} #TODO: consider formalising Records function in bedgraph (e.g. Bedgraph.Records, Bedgraph.Bedgraph.Records) that returns Vector{Bedgraph.Record}.
+    cols, names = create_columns_from_iterabletable(x, na_representation=:missing)
+
+    return convert(Vector{Bedgraph.Record}, cols[1], cols[2], cols[3], cols[4])
+end
+
+function Vector{Bedgraph.Record}(x::AbstractVector{T}) :: Vector{Bedgraph.Record} where {T<:NamedTuple}
+    @debug "Vector{Bedgraph.Record}(x::AbstractVector{T})"
+    return  _Records(x)
+end
+
+function Vector{Bedgraph.Record}(file::B) :: Vector{Bedgraph.Record} where {B<:BedgraphFile}
+    @debug "Vector{Bedgraph.Record}(file::BedgraphFile)"
+    return _loaddata(file.filename)
+end
+
+function Vector{Bedgraph.Record}(x::T) :: Vector{Bedgraph.Record} where {T} #TODO: consider formalising Records function in bedgraph (e.g. Bedgraph.Records, Bedgraph.Bedgraph.Records) that returns Vector{Bedgraph.Record}.
+
+    if TableTraits.isiterabletable(x)
+        @debug "Vector{Bedgraph.Record}(x) - isiterabletable"
+        return _Records(x)
+    else
+        @debug "Vector{Bedgraph.Record}(x) - converting"
+        return convert(Vector{Bedgraph.Record}, x)
+    end
+end
+
+function save(file::BedgraphFileFormat, header::Bedgraph.BedgraphHeader, records::Vector{Bedgraph.Record}) :: Vector{Bedgraph.Record}
+
     write(file.filename, header, records)
+
+    return records #Note: this return is useful when piping (e.g., records = some_operation | save(file)).
 end
 
-function save(file::BedgraphFileFormat, records::Vector{Bedgraph.Record}; bump_forward = true)
+function save(file::BedgraphFileFormat, records::Vector{Bedgraph.Record}; bump_forward = true) :: Vector{Bedgraph.Record}
 
-    #TODO: bump_forward records.
+    sort!(records)
 
-    header = Bedgraph.generateBasicHeader(records, bump_forward = bump_forward)
+    header = Bedgraph.generateBasicHeader(records, bump_forward = bump_forward) #TODO: consolidate header generation and determine whether there is a need for bump_forward.
 
     return save(file, header, records)
 end
 
 function save(file::BedgraphFileFormat, data; bump_forward = true)
-    isiterabletable(data) || error("Can't write this data to bedGraph file.")
 
     it = getiterator(data)
 
-    df = DataFrame(it)
+    records = Vector{Bedgraph.Record}(it)
 
-    # Pack DataFrame in to a vector of type record.
-    records = Vector{Bedgraph.Record}(undef, length(it))
+    save(file, records, bump_forward = bump_forward)
 
-    for (i, row) in enumerate(eachrow(df))
-        records[i] =  Bedgraph.Record(row[1], row[2], row[3], row[4]) # Note: using index to allow flexible column names.
-    end
-
-    header = Bedgraph.generateBasicHeader(records, bump_forward = bump_forward)
-
-    return save(file, header, records)
+    return data #Note: this return is usful when piping.
 end
 
 end # module