Use new BioGenerics macros

Project.toml

@@ -3,9 +3,6 @@ uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 authors = ["Sabrina J. Ward <[email protected]>", "Jakob N. Nissen <[email protected]>"]
 version = "2.1.3"
 
-[weakdeps]
-BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
@@ -14,23 +11,27 @@ PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 StringViews = "354b36f9-a18e-4713-926e-db85100087ba"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
+[weakdeps]
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+
 [extensions]
 BioSequencesExt = "BioSequences"
 
 [compat]
 Automa = "1"
-BioGenerics = "0.1.2"
+BioGenerics = "0.1.3"
 BioSequences = "3"
 PrecompileTools = "1"
 StringViews = "1"
 TranscodingStreams = "0.9.5"
 julia = "1.6"
 
 [extras]
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["BioSequences", "Random", "Test", "FormatSpecimens"]
+test = ["BioSequences", "CodecZlib", "Random", "Test", "FormatSpecimens"]

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/src/files.md

@@ -75,6 +75,8 @@ UInt8[]
 ```
 
 To use it correctly, either call `flush`, or close the writer first (which also closes the underlying stream).
+
+### Readers and writers with do-syntax
 It is recommended to use readers and writers to `do` syntax in the form:
 ```jldoctest
 julia> FASTAWriter(open(tempname(), "w")) do writer
@@ -95,6 +97,34 @@ julia> open(FASTAWriter, tempname()) do writer
 
 However, this latter syntax does not easily extend to different types of IO, such as gzip compressed streams.
 
+However, this latter syntax does not easily extend to different types of IO, such as gzip compressed streams.
+
+### `rdr` and `wtr` macros
+The `rdr` and `wtr` macros use the passed file name to determine the FASTX reader or writer to use - including any compression file extensions.
+Since this both uses heuristics, and the macro is a little opaque to users, it is recommended to use these macros for ephemeral REPL work, and not in packages where the more explicit forms are preferred.
+
+The macro call `rdr"seqs.fna.gz"` expands to
+```julia
+FASTAReader(GzipDecompressorStream(open("seqs.fna.gz"; lock=false)))
+```
+
+Even though the reader (or writer) is already opened, you can still use the ordinary `open(x) do f`
+pattern to automatically close the reader when done:
+
+```jldoctest
+julia> using CodecZlib # for gzip files
+
+julia> open(rdr"../test/data/test.fasta") do reader
+           println(identifier(first(reader)))
+       end
+abc
+
+julia> open(wtr"seqs.fna.gz") do writer 
+           write(writer, FASTARecord("my_header", "TAGAG"))
+       end
+17
+```
+
 ### Validate files
 The functions `validate_fasta` and `validate_fastq` can be used to check if an `IO`
 contains data that can be read as FASTX.

docs/src/index.md

@@ -75,6 +75,22 @@ julia> FASTQWriter(GzipCompressorStream(open(tempname(), "w"))) do writer
 28
 ```
 
+For added convenience, you can also use the reader and writer macros `rdr""` and `wtr""`.
+These macros use the file extensions to determine the biological sequence reader or writer type, and any file compresion.
+To use these macros with the `do`-syntax, you can use `open` as normal. Hence, the above code block can also be written in the following equivalent way:
+
+```jldoctest
+julia> using CodecZlib
+
+julia> open(rdr"../test/data/seqs.fna.gz") do reader
+           for record in reader
+               println(identifier(record))
+           end
+       end
+seqa
+seqb
+```
+
 ### Construct FASTA or FASTQ records from raw parts
 ```jldoctest
 julia> fasta_record = FASTARecord("some header", dna"TAGAAGA");

src/FASTX.jl

@@ -2,6 +2,7 @@ module FASTX
 
 using StringViews: StringView
 using Automa: Automa
+using BioGenerics: BioGenerics, @rdr_str, @wtr_str
 
 """
     identifier(record::Record)::AbstractString
@@ -220,6 +221,11 @@ const FASTQReader = FASTQ.Reader
 const FASTAWriter = FASTA.Writer
 const FASTQWriter = FASTQ.Writer
 
+const FASTA_EXTENSIONS = Union{Val{:fa}, Val{:fasta}, Val{:faa}, Val{:fna}}
+
+BioGenerics.readertype(::FASTA_EXTENSIONS, arg) = FASTAReader
+BioGenerics.writertype(::FASTA_EXTENSIONS, arg) = FASTAWriter
+
 if !isdefined(Base, :get_extension)
     include("../ext/BioSequencesExt.jl")
   end
@@ -249,6 +255,10 @@ export
     faidx,
     index!,
     extract,
-    seekrecord
+    seekrecord,
+
+    # Re-export from BioGenerics
+    @rdr_str,
+    @wtr_str
 
 end # module

test/maintests.jl

@@ -1,3 +1,5 @@
+using CodecZlib
+
 # Common tests
 @testset "FASTX" begin
     @testset "Copying to LongSequence" begin
@@ -133,4 +135,4 @@
         @test sequence(fq) == "TAGJKKm"
         @test quality(fq) == "jjkkmmo"
     end
-end
+end