Contents

require 'genomer'
require 'genomer-plugin-summary/metrics'
require 'genomer-plugin-summary/format'

class GenomerPluginSummary::Genome < Genomer::Plugin
  include GenomerPluginSummary::Metrics
  include GenomerPluginSummary::Format

  LAYOUT = [
    {:name => 'Sequences (#)', :entry_type => :sequence,  :method => :count},
    {:name => 'Contigs (#)',   :entry_type => :contig,    :method => :count},
    {:name => 'Gaps (#)',      :entry_type => :gap,       :method => :count},
    :separator,
    {:name => 'Size (bp)',      :entry_type => :all,      :method => :length},
    {:name => 'Sequences (bp)', :entry_type => :sequence, :method => :length},
    {:name => 'Contigs (bp)',   :entry_type => :contig,   :method => :length},
    {:name => 'Gaps (bp)',      :entry_type => :gap,      :method => :length},
    :separator,
    {:name => 'G+C (%)',        :entry_type => :all,      :method => :gc_content},
    {:name => 'Sequences (%)',  :entry_type => :sequence, :method => :percent},
    {:name => 'Contigs (%)',    :entry_type => :contig,   :method => :percent},
    {:name => 'Gaps (%)',       :entry_type => :gap,      :method => :percent}
  ]

  FORMATTING = {
    :title         => 'Scaffold',
    :width         => {0 => 12, 1 => 9},
    :justification => {1 => :right},
    :format        => {1 => lambda{|i| i.class == Float ? sprintf('%#.2f',i) : i }}
  }

  def run
    tabulate(calculate_metrics(LAYOUT, scaffold),flags)
  end

  def tabulate(data,flags)
    FORMATTING.store(:output,flags[:output]) if flags[:output]
    table(data,FORMATTING)
  end

  def calculate_metrics(specs,scaffold)
    specs.map do |spec|
      if spec == :separator
        spec
      else
        [spec[:name], send(spec[:method],spec[:entry_type],scaffold)]
      end
    end
  end

end

Version data entries

2 entries across 2 versions & 1 rubygems

Version	Path
genomer-plugin-summary-0.0.5	lib/genomer-plugin-summary/genome.rb
genomer-plugin-summary-0.0.4	lib/genomer-plugin-summary/genome.rb