bio-fastqc 0.4.2 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: dcf2df85ad7a71c557b850db952a254e2267c934
+  metadata.gz: fbe1e9dae94ae5c33532fd6f90c0e576494ff6ee
+  data.tar.gz: 5adde2e4c5b8ac16dd36954756401386910d3f54
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+  metadata.gz: 530320b194014e5e3a8474afce4ca62a1c1ea6e900963a0379d0d762d92d69440be9dc41ea163a43f816c31589d60ab30311bc6d7e859512d61ea57f36bdef4c
+  data.tar.gz: a1711287c08560be9c8827b33ae3295de2252703236333003b4b7c0a49257060d32da091447185af959f8e5d1a94b2fd1215d907a635087598337b3ddf965509

data/VERSION

@@ -1 +1 @@
-0.4.2
+0.5.0

data/lib/bio/fastqc/cli.rb

@@ -6,7 +6,7 @@ require 'json'
 module Bio
   module FastQC
     class CLI < Thor
-      desc "parse [--format format] [filename]", "parse fastqc data in fastqc directory or zipfile, output in json, json-ld, or rdf-turtle format."
+      desc "parse [--format format] [filename]", "parse fastqc data in fastqc directory or zipfile. output format: json (--json), json-ld (--jsonld), rdf-turtle (--ttl), or one-line tsv format (--tsv)."
       option :format, :default => "json"
       def parse(file)
         data = Data.read(file)

data/lib/bio/fastqc/converter.rb

@@ -16,6 +16,8 @@ module Bio
           to_jsonld
         when "turtle"
           to_turtle
+        when "tsv"
+          to_tsv
         end
       end
 
@@ -40,6 +42,35 @@ module Bio
       def to_ttl
         to_turtle
       end
+
+      def to_tsv
+        identifier = if @id
+                       @id
+                     else
+                       @summary_json[:filename].split(".").first
+                     end
+
+        # return one-line tab separated value
+        [
+          identifier,
+          @summary_json[:fastqc_version],
+          @summary_json[:filename],
+          @summary_json[:file_type],
+          @summary_json[:encoding],
+          @summary_json[:total_sequences],
+          @summary_json[:filtered_sequences],
+          @summary_json[:sequence_length],
+          @summary_json[:min_length],
+          @summary_json[:max_length],
+          @summary_json[:mean_sequence_length],
+          @summary_json[:median_sequence_length],
+          @summary_json[:percent_gc],
+          @summary_json[:total_duplicate_percentage],
+          @summary_json[:overall_mean_quality_score],
+          @summary_json[:overall_median_quality_score],
+          @summary_json[:overall_n_content],
+        ].join("\t")
+      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-fastqc
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.5.0
 platform: ruby
 authors:
 - Tazro Inutano Ohta
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-16 00:00:00.000000000 Z
+date: 2016-03-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip