Class: Ciika::SRA::Experiment

Inherits:
Object
  • Object
show all
Defined in:
lib/ciika/sra/experiment.rb

Instance Method Summary collapse

Constructor Details

#initialize(xml, id: :all) ⇒ Experiment

Returns a new instance of Experiment.

Raises:

  • (NameError) 


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# File 'lib/ciika/sra/experiment.rb', line 6

def initialize(xml, id: :all)
  @experimentset = Ciika::SRA::id_selector("EXPERIMENT", xml, id)
  raise NameError, "ID not found" if @studyset == []
end

Instance Method Details

#parse ⇒ Object 



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# File 'lib/ciika/sra/experiment.rb', line 11

def parse
  @experimentset.map do |experiment|
    layout = experiment.css("LIBRARY_LAYOUT").first.children[1]
    {
      accession:          experiment.attr("accession").to_s,
      alias:              experiment.attr("alias").to_s,
      center_name:        experiment.attr("center_name").to_s,
      title:              experiment.css("TITLE").inner_text,
      study_accession:    experiment.css("STUDY_REF").attr("accession").to_s,
      study_refname:      experiment.css("STUDY_REF").attr("refname").to_s,
      design_description: experiment.css("DESIGN_DESCRIPTION").inner_text,
      sample_accession:   experiment.css("SAMPLE_DESCRIPTOR").first.attr("accession").to_s,
      sample_refname:     experiment.css("SAMPLE_DESCRIPTOR").first.attr("refname").to_s,

      library_description: {
        library_name:                  experiment.css("LIBRARY_NAME").inner_text,
        library_strategy:              experiment.css("LIBRARY_STRATEGY").inner_text,
        library_source:                experiment.css("LIBRARY_SOURCE").inner_text,
        library_selection:             experiment.css("LIBRARY_SELECTION").inner_text,
        library_layout:                experiment.css("LIBRARY_LAYOUT").first.children[1].name,
        library_orientation:           layout.attr("ORIENTATION").to_s,
        library_nominal_length:        layout.attr("NOMINAL_LENGTH").to_s,
        library_nominal_sdev:          layout.attr("NOMINAL_SDEV").to_s,
        library_construction_protocol: experiment.css("LIBRARY_CONSTRUCTION_PROTOCOL").inner_text,
      },

      platform_information:   {
        platform:         experiment.css("PLATFORM").first.children[1].name,
        instrument_model: experiment.css("INSTRUMENT_MODEL").inner_text,
        cycle_sequence:   experiment.css("CYCLE_SEQUENCE").inner_text,
        cycle_count:      experiment.css("CYCLE_COUNT").inner_text,
        flow_sequence:    experiment.css("FLOW_SEQUENCE").inner_text,
        flow_count:       experiment.css("FLOW_COUNT").inner_text,
        key_sequence:     experiment.css("KEY_SEQUENCE").inner_text,
      },

      processing_information: {
        base_calls: {
          sequence_space: experiment.css("SEQUENCE_SPACE").inner_text,
          base_caller:    experiment.css("BASE_CALLER").inner_text,
        },

        quality_scores: experiment.css("QUALITY_SCORES").map{|node|
          {
            quality_type:    node.attr("qtype").to_s,
            quality_scorer:  node.css("QUALITY_SCORER").inner_text,
            number_of_level: node.css("NUMBER_OF_LEVELS").inner_text,
            multiplier:      node.css("MULTIPLIER").inner_text
          }
        },

        pipe_section:   experiment.css("PIPE_SECTION").map{|node|
          {
            step_index:      node.css("STEP_INDEX").inner_text,
            prev_step_index: node.css("PREV_STEP_INDEX").inner_text,
            program:         node.css("PROGRAM").inner_text,
            version:         node.css("VERSION").inner_text,
          }
        },
      },

      spot_information: {
        number_of_reads_per_spot: experiment.css("NUMBER_OF_READS_PER_SPOT").inner_text,
        spot_length:              experiment.css("SPOT_LENGTH").inner_text,
      },

      read_spec: experiment.css("READ_SPEC").map{|node|
        {
          read_index: node.css("READ_INDEX").inner_text,
          read_class: node.css("READ_CLASS").inner_text,
          read_type: node.css("READ_TYPE").inner_text,
          base_coord: node.css("BASE_COORD").inner_text,
        }
      },
    }
  end
end