Class: GenomerPluginView::Table

Inherits:
Genomer::Plugin
  • Object
show all
Defined in:
lib/genomer-plugin-view/table.rb

Constant Summary collapse

SUPPORTED_FEATURE_TYPES = 
['CDS','rRNA','tRNA','miscRNA','tmRNA']

Instance Method Summary collapse

Instance Method Details

#create_encoded_features(genes, prefix) ⇒ Object 



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# File 'lib/genomer-plugin-view/table.rb', line 21

def create_encoded_features(genes,prefix)
  features = genes.map do |gene|
    feature = gene.clone
    attrs   = feature.attributes.clone

    feature_type    = attrs.detect{|k,v| k == 'feature_type'}
    feature.feature = (feature_type ? feature_type.last : 'CDS')

    unless SUPPORTED_FEATURE_TYPES.include?(feature.feature)
      raise Genomer::Error, "Unknown feature_type '#{feature.feature}'"
    end

    attrs.map! do |(k,v)|
      v = (k == 'ID' && prefix.instance_of?(String) ? prefix + v : v)
      [k,v]
    end

    if feature.feature == "CDS"

      if attrs.detect{|(k,v)| k == 'Name' }
        attrs.map! do |(k,v)|
          v      = v.clone
          v[0,1] = v[0,1].upcase if k == 'Name'

          v = nil                if k == 'function'
          k = 'function'         if k == 'product'
          k = 'product'          if k == 'Name'
          [k,v]
        end
      end
      #attrs.delete('Name')
    end

    feature.attributes = attrs.reject{|(_,value)| value.nil? }
    feature
  end
  genes.zip(features).flatten
end

#run ⇒ Object 



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# File 'lib/genomer-plugin-view/table.rb', line 6

def run
  options = GenomerPluginView.convert_command_line_flags(flags)

  header = ">Feature\t#{options[:identifier]}\tannotation_table\n"

  attns = annotations(options)
  attns = create_encoded_features(attns, options[:encoded]) if options[:encoded]

  attns.inject(header) do |table,attn|
    table << attn.to_genbank_table_entry
  end
end