bio-fastqc 0.5.1 → 0.5.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: a4de37536fda8307419ca4307f6cde421dbe64a3
+  metadata.gz: 24e302a0001de21bb4e1ad93ef748b397a5758c9
+  data.tar.gz: a3fecf79186d42870c47aa5f03595dc62d5c15fc
 SHA512:
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+  data.tar.gz: 2441701ea9d0761bf2f9aac4ae5b9cdb7ab3d3f55270630d4ba9b1158f1dd26107b8812e8c97282541bf0f904df9e8f460047c97bf5c7a61ffe0b80c0ed40381

data/VERSION

@@ -1 +1 @@
-0.5.1
+0.5.2

data/lib/bio-fastqc.rb

@@ -8,6 +8,7 @@
 #
 # In this file only require other files. Avoid other source code.
 
+require 'bio/fastqc/io'
 require 'bio/fastqc/data'
 require 'bio/fastqc/cli'
 require 'bio/fastqc/parser'

data/lib/bio/fastqc/io.rb

@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+
+require 'rdf/turtle'
+
+module Bio
+  module FastQC
+    class IO
+      def initialize(summary_json, id: nil)
+        @summary_json = summary_json
+        @id = id
+      end
+
+      def write(output_file, format)
+        case format
+        when "json"
+          write_json(output_file)
+        when "json-ld", "jsonld"
+          write_jsonld(output_file)
+        when "turtle", "ttl"
+          write_ttl(output_file)
+        when "tsv"
+          write_tsv(output_file)
+        end
+      end
+
+      def write_json(output_file)
+        json = Converter.new(@summary_json, id: @id).to_json
+        open(output_file, 'w'){|file| file.puts(json) }
+      end
+
+      def write_jsonld(output_file)
+        jsonld = Converter.new(@summary_json, id: @id).to_jsonld
+        open(output_file, 'w'){|file| file.puts(jsonld) }
+      end
+
+      def write_ttl(output_file)
+        semantics = Semantics.new(@summary_json, id: @id)
+        graph = semantics.turtle_graph
+        prefixes = semantics.turtle_prefixes
+        RDF::Turtle::Writer.open(output_file, prefixes: prefixes) do |writer|
+          writer << graph
+        end
+      end
+
+      def write_tsv(output_file)
+        tsv = Converter.new(@summary_json, id: @id).to_tsv
+        open(output_file, 'w'){|file| file.puts(tsv) }
+      end
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-fastqc
 version: !ruby/object:Gem::Version
-  version: 0.5.1
+  version: 0.5.2
 platform: ruby
 authors:
 - Tazro Inutano Ohta
@@ -224,6 +224,7 @@ files:
 - lib/bio/fastqc/cli.rb
 - lib/bio/fastqc/converter.rb
 - lib/bio/fastqc/data.rb
+- lib/bio/fastqc/io.rb
 - lib/bio/fastqc/parser.rb
 - lib/bio/fastqc/semantics.rb
 - spec/bio-fastqc_spec.rb