added FileIO interface

Project.toml

@@ -13,6 +13,12 @@ GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 Indexes = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
+[weakdeps]
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+
+[extensions]
+FileIOExt = "FileIO"
+
 [compat]
 Automa = "1"
 BGZFStreams = "0.3"
@@ -30,6 +36,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 
 [targets]
-test = ["Distributions", "Documenter", "FormatSpecimens", "Random", "Test"]
+test = ["Distributions", "Documenter", "FormatSpecimens", "Random", "Test", "FileIO"]

ext/FileIOExt.jl

@@ -0,0 +1,34 @@
+module FileIOExt
+
+using BED, FileIO
+
+function BED.fileio_load(filepath::File{format"BED"})
+
+    reader = open(BED.Reader, FileIO.filename(filepath))
+    records = try 
+        records = [record for record in reader]
+    catch err
+        close(reader)
+        rethrow(err)
+    end
+    close(reader)
+
+    records
+end
+
+function BED.fileio_save(filepath::File{format"BED"}, records)
+
+    writer = open(BED.Writer, FileIO.filename(filepath))
+    try 
+        for record in records
+            write(writer, record)
+        end
+    catch err
+        close(writer)
+        rethrow(err)
+    end
+    close(writer)
+    filepath
+end
+
+end

src/BED.jl

@@ -15,4 +15,8 @@ include("record.jl")
 include("reader.jl")
 include("writer.jl")
 
+# placeholder for FileIO interface
+fileio_load() = nothing
+fileio_save() = nothing
+
 end # module

test/runtests.jl

@@ -6,6 +6,7 @@ using Distributions
 using Documenter
 using FormatSpecimens
 using GenomicFeatures
+using FileIO
 
 import Random
 import ColorTypes: RGB
@@ -130,7 +131,7 @@ end
             continue
         end
 
-        filepath = joinpath(dir_bed, filename(specimen))
+        filepath = joinpath(dir_bed, FormatSpecimens.filename(specimen))
 
         @test check_bed_parse(filepath)
 
@@ -143,7 +144,7 @@ end
             continue
         end
 
-        filepath = joinpath(dir_bed, filename(specimen))
+        filepath = joinpath(dir_bed, FormatSpecimens.filename(specimen))
 
         @test_throws Exception check_bed_parse(filepath)
     end
@@ -285,6 +286,26 @@ end
         @test isa(BED.Reader(path), BED.Reader)
     end
 
+    @testset "FileIO" begin
+
+        dir_bed = path_of_format("BED")
+
+        for specimen in list_valid_specimens("BED")
+            if hastag(specimen, "gzip")
+                # skip compressed files
+                continue
+            end
+
+            mktempdir() do dir
+                filepath = joinpath(dir_bed, FormatSpecimens.filename(specimen))
+                records = FileIO.load(filepath)
+
+                FileIO.save(joinpath(dir, "tmp.bed"), records)
+                @test [record for record in open(BED.Reader, filepath)] == records
+            end
+        end
+    end
+
     # Include doctests.
     DocMeta.setdocmeta!(BED, :DocTestSetup, :(using BED); recursive=true)
     doctest(BED; manual = false)