Class: GenomerPluginSummary::Gaps

Inherits:
Genomer::Plugin
  • Object
show all
Includes:
Format
Defined in:
lib/genomer-plugin-summary/gaps.rb

Constant Summary collapse

COLUMNS = 
[:number,  :length,  :start,  :end,  :type]
FORMATTING = 
{
  :title   => 'Scaffold Gaps',
  :headers => ['Number', 'Length', 'Start', 'End', 'Type'],
  :width   => {
    0 => 8,
    1 => 8,
    2 => 8,
    3 => 8,
    4 => 12
  },
  :justification   => {
    0 => :right,
    1 => :right,
    2 => :right,
    3 => :right,
    4 => :center
  }
}

Constants included from Format

Format::DEFAULTS

Instance Method Summary collapse

Methods included from Format

#create_cells, #csv, #format_cell, #pretty, #table

Instance Method Details

#determine_gaps(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/gaps.rb', line 43

def determine_gaps(scaffold)
  count  = 0
  length = 0

  scaffold.map do |entry|
    gaps = case entry.entry_type
           when :sequence then
             gap_locations(entry.sequence).map do |gap|
               count += 1
               {:number => count,
                :length => (gap.end - gap.begin) + 1,
                :start  => gap.begin + length,
                :end    => gap.end   + length,
                :type   => :contig}
             end
           when :unresolved then
             count += 1
             {:number => count,
              :length => entry.sequence.length,
              :start  => length + 1,
              :end    => length + entry.sequence.length,
              :type   => :unresolved}
           end
    length += entry.sequence.length
    gaps
  end.flatten
end

#gap_locations(seq) ⇒ Object 



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# File 'lib/genomer-plugin-summary/gaps.rb', line 37

def gap_locations(seq)
  seq.upcase.enum_for(:scan, /(N+)/).map do
    (Regexp.last_match.begin(0)+1)..(Regexp.last_match.end(0))
  end
end

#run ⇒ Object 



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# File 'lib/genomer-plugin-summary/gaps.rb', line 7

def run
  tabulate(determine_gaps(scaffold),flags)
end

#tabulate(gaps, flags) ⇒ Object 



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# File 'lib/genomer-plugin-summary/gaps.rb', line 32

def tabulate(gaps,flags)
  FORMATTING[:output] = flags[:output]
  table(gaps.map{|gap| COLUMNS.map{|col| gap[col]}},FORMATTING)
end