class Bio::FastQC::Converter
Public Class Methods
new(fastqc_object, id: nil, runid: nil)
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# File lib/bio/fastqc/converter.rb, line 5 def initialize(fastqc_object, id: nil, runid: nil) @id = id @runid = runid @fastqc_object = fastqc_object end
Public Instance Methods
convert_to(format)
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# File lib/bio/fastqc/converter.rb, line 11 def convert_to(format) case format when "json" to_json when "json-ld", "jsonld" to_jsonld when "turtle", "ttl" to_turtle when "tsv" to_tsv end end
to_json()
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# File lib/bio/fastqc/converter.rb, line 24 def to_json json = if @id { @id => @fastqc_object } else @fastqc_object end JSON.dump(json) end
to_jsonld()
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# File lib/bio/fastqc/converter.rb, line 33 def to_jsonld json_ld_object = Semantics.new(@fastqc_object, id: @id, runid: @runid).json_ld_object JSON.dump(json_ld_object) end
to_tsv()
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# File lib/bio/fastqc/converter.rb, line 46 def to_tsv identifier = if @id @id else @fastqc_object[:filename].split(".").first end # return one-line tab separated value [ identifier, @fastqc_object[:fastqc_version], @fastqc_object[:filename], @fastqc_object[:file_type], @fastqc_object[:encoding], @fastqc_object[:total_sequences], @fastqc_object[:filtered_sequences], @fastqc_object[:sequence_length], @fastqc_object[:min_length], @fastqc_object[:max_length], @fastqc_object[:mean_sequence_length], @fastqc_object[:median_sequence_length], @fastqc_object[:percent_gc], @fastqc_object[:total_duplicate_percentage], @fastqc_object[:overall_mean_quality_score], @fastqc_object[:overall_median_quality_score], @fastqc_object[:overall_n_content], ].join("\t") end
to_ttl()
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# File lib/bio/fastqc/converter.rb, line 42 def to_ttl to_turtle end
to_turtle()
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# File lib/bio/fastqc/converter.rb, line 38 def to_turtle Semantics.new(@fastqc_object, id: @id, runid: @runid).turtle end