Contents

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

class GenomerPluginSummary::Contigs < Genomer::Plugin
  include GenomerPluginSummary::Metrics
  include GenomerPluginSummary::Format
  include GenomerPluginSummary::Enumerators

  FORMATTING = {
    :title   => 'Scaffold Contigs',
    :headers => ['Contig', 'Start (bp)', 'End (bp)', 'Size (bp)', 'Size (%)', 'GC (%)'],
    :width => {
      0 => 6,
      1 => 10,
      2 => 10,
      3 => 10,
      4 => 8,
      5 => 6
    },
    :justification => {
      0 => :right,
      1 => :right,
      2 => :right,
      3 => :right,
      4 => :right,
      5 => :right
    },
    :format => {
      4 => '%#.2f',
      5 => '%#.2f'
    }
  }
  COLUMNS = [:id, :start, :stop, :size, :percent, :gc]

  def run
    contigs = calculate(scaffold)
    total   = sequence_total(contigs)

    tabulate(contigs,total,flags)
  end

  def tabulate(contigs,total,flags)
    rows = contigs.map{|contig| COLUMNS.map{|col| contig[col]}}.
      <<(:separator).
      <<(COLUMNS.map{|col| total[col] || 'All'})

    FORMATTING[:output] = flags[:output]
    table(rows,FORMATTING)
  end

  def calculate(scaffold)
    total_length = scaffold.mapping(&:sequence).mapping(&:length).inject(&:+).to_f
    enumerator_for_contig(scaffold).
      mapping{|i| i[:gc] = gc(i[:sequence]) / atgc(i[:sequence]) * 100; i}.
      mapping{|i| i[:size] = i[:sequence].length; i}.
      mapping{|i| i[:percent] = i[:size] / total_length * 100; i}.
      mapping{|i| i.delete(:sequence); i}.
      to_a
  end

end

Version data entries

2 entries across 2 versions & 1 rubygems

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