Class: Bio::FastQC::IO

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/fastqc/io.rb

Instance Method Summary collapse

Constructor Details

#initialize(fastqc_object, id: nil) ⇒ IO

Returns a new instance of IO.



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# File 'lib/bio/fastqc/io.rb', line 8

def initialize(fastqc_object, id: nil)
  @fastqc_object = fastqc_object
  @id = id
end

Instance Method Details

#write(output_file, format) ⇒ Object 



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# File 'lib/bio/fastqc/io.rb', line 13

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

#write_json(output_file) ⇒ Object 



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# File 'lib/bio/fastqc/io.rb', line 26

def write_json(output_file)
  json = Converter.new(@fastqc_object, id: @id).to_json
  open(output_file, 'w'){|file| file.puts(json) }
end

#write_jsonld(output_file) ⇒ Object 



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# File 'lib/bio/fastqc/io.rb', line 31

def write_jsonld(output_file)
  jsonld = Converter.new(@fastqc_object, id: @id).to_jsonld
  open(output_file, 'w'){|file| file.puts(jsonld) }
end

#write_tsv(output_file) ⇒ Object 



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# File 'lib/bio/fastqc/io.rb', line 45

def write_tsv(output_file)
  tsv = Converter.new(@fastqc_object, id: @id).to_tsv
  open(output_file, 'w'){|file| file.puts(tsv) }
end

#write_ttl(output_file) ⇒ Object 



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# File 'lib/bio/fastqc/io.rb', line 36

def write_ttl(output_file)
  semantics = Semantics.new(@fastqc_object, id: @id)
  graph = semantics.turtle_graph
  prefixes = semantics.turtle_prefixes
  RDF::Turtle::Writer.open(output_file, prefixes: prefixes) do |writer|
    writer << graph
  end
end