Merge branch 'release/v1.0.0'

README.md

@@ -1,10 +1,11 @@
-# BedgraphFiles
+# BedgraphFiles.jl
 
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![Build Status](https://travis-ci.org/CiaranOMara/BedgraphFiles.jl.svg?branch=master)](https://travis-ci.org/CiaranOMara/BedgraphFiles.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/jny2ep4u3cmly8pj/branch/master?svg=true)](https://ci.appveyor.com/project/CiaranOMara/Bedgraphfiles-jl/branch/master)
 [![BedgraphFiles](http://pkg.julialang.org/badges/BedgraphFiles_0.6.svg)](http://pkg.julialang.org/?pkg=BedgraphFiles)
 [![codecov.io](http://codecov.io/github/CiaranOMara/BedgraphFiles.jl/coverage.svg?branch=master)](http://codecov.io/github/CiaranOMara/BedgraphFiles.jl?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/CiaranOMara/BedgraphFiles.jl/badge.svg?branch=master)](https://coveralls.io/github/CiaranOMara/BedgraphFiles.jl?branch=master)
 
 ## Overview
 

REQUIRE

@@ -1,4 +1,5 @@
 julia 0.6
-IterableTables 0.4.2
+TableTraits 0.0.1
+IterableTables 0.5.0
 FileIO 0.5.1
-DataFrames 0.9.1
+DataFrames 0.9.0

src/BedgraphFiles.jl

@@ -1,8 +1,9 @@
 module BedgraphFiles
 
 # using Bedgraph
-using IterableTables, DataValues, DataFrames
+using TableTraits, DataValues, DataFrames
 using FileIO
+import IterableTables
 
 try add_format(format"Bedgraph", (), [".bedgraph"], [:BedgraphFiles]) end # TODO: Remove once BedgraphFiles is registered with FileIO.
 
@@ -14,17 +15,18 @@ function load(f::FileIO.File{FileIO.format"Bedgraph"})
     return BedgraphFile(f.filename)
 end
 
-IterableTables.isiterable(x::BedgraphFile) = true
-IterableTables.isiterabletable(x::BedgraphFile) = true
+TableTraits.isiterable(x::BedgraphFile) = true
+TableTraits.isiterabletable(x::BedgraphFile) = true
 
-function IterableTables.getiterator(file::BedgraphFile)
+function TableTraits.getiterator(file::BedgraphFile)
 
     # TODO: read using bedgraph package.
     # df = Bedgraph.read(file.filename, DataFrame)
 
     data = readdlm(file.filename)
 
-    df = DataFrame(Chromosome=data[:,1], Start=data[:,2], End=data[:,3], Value=data[:,4])
+    # Track data format: chrom chromStart chromEnd dataValue
+    df = DataFrame(chrom=data[:,1], chromStart=data[:,2], chromEnd=data[:,3], dataValue=data[:,4])
 
     it = getiterator(df)
 
@@ -46,7 +48,7 @@ function save(f::FileIO.File{FileIO.format"Bedgraph"}, data)
     # end
 
     try
-        output = [convert(Array,it.df[:Chromosome]) convert(Array,it.df[:Start]) convert(Array,it.df[:End]) convert(Array,it.df[:Value]) ]
+        output = [convert(Array,it.df[:chrom]) convert(Array,it.df[:chromStart]) convert(Array,it.df[:chromEnd]) convert(Array,it.df[:dataValue]) ]
 
         writedlm(f.filename, output)
     end

test/runtests.jl

@@ -1,28 +1,53 @@
 using FileIO
-using IterableTables
-using BedgraphFiles
+using TableTraits
 using DataFrames
 using Base.Test
 
+try add_format(format"Bedgraph", (), [".bedgraph"], [:BedgraphFiles]) end # TODO: Remove once files is registered with FileIO.
+
 @testset "BedgraphFiles" begin
 
-df = load(joinpath(@__DIR__, "data.bedgraph")) |> DataFrame
+const chrom = ["chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19"]
+const chromStart = [49302000, 49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400]
+const chromEnd = [49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400, 49304700]
+const dataValue = [-1.0, -0.75, -0.50, -0.25, 0.0, 0.25, 0.50, 0.75, 1.00]
+
+file = joinpath(@__DIR__, "data.bedgraph")
+
+@test isfile(file)
+
+# Load tests.
+loaded = load(file)
+@test isiterable(loaded) == true
+
+## DataFrame
+df = DataFrame(loaded)
 
 @test size(df) == (9,4)
 
-@test df[:Chromosome] == ["chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19", "chr19"]
-@test df[:Start] == [49302000, 49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400]
-@test df[:End] == [49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400, 49304700]
-@test df[:Value] == [-1.0, -0.75, -0.50, -0.25, 0.0, 0.25, 0.50, 0.75, 1.00]
+@test df[:chrom] == chrom
+@test df[:chromStart] == chromStart
+@test df[:chromEnd] == chromEnd
+@test df[:dataValue] == dataValue
+
+## Query DataFrame
+df2 = loaded |> DataFrame
+@test size(df2) == (9,4)
+
+@test df2[:chrom] == chrom
+@test df2[:chromStart] == chromStart
+@test df2[:chromEnd] == chromEnd
+@test df2[:dataValue] == dataValue
 
+# Save test.
 output_filename = tempname() * ".bedgraph"
 
 try
     df |> save(output_filename)
 
-    df2 = load(output_filename) |> DataFrame
+    loaded_df = load(output_filename) |> DataFrame
 
-    @test df == df2
+    @test df == loaded_df
 finally
     gc()
     rm(output_filename)