Class: GenomerPluginView::Agp

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

Instance Method Summary collapse

Instance Method Details

#contig(length, cum, count, no) ⇒ Object 



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# File 'lib/genomer-plugin-view/agp.rb', line 54

def contig(length, cum, count, no)
  %W|scaffold #{cum} #{cum + length} #{count} W #{sprintf("contig%05d",no)} 1 #{length+1} +| * "\t"
end

#entries ⇒ Object 



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# File 'lib/genomer-plugin-view/agp.rb', line 16

def entries
  cumulative_length  = 1
  count   = 0
  contigs = 0

  scaffold.map do |entry|
    case entry.entry_type
    when :unresolved then
      length = entry.sequence.length
      count += 1
      start = cumulative_length
      stop  = cumulative_length += length
      gap(start, stop - 1, count, 'specified')
    when :sequence   then
      seq = entry.sequence.upcase
      seq_regions = locations(seq,/[^N]+/).map{|i| [:contig,i]}
      gap_regions = locations(seq,/N+/).map{|i| [:gap,i]}
      entries = (seq_regions + gap_regions).sort_by{|_,loc| loc.to_a}

      entries.map do |(type,location)|
        count += 1
        length = (location.end - location.begin)
        entry = case type
                when :contig then
                  contigs += 1
                  contig(length, cumulative_length, count, contigs)
                when :gap    then
                  start = cumulative_length
                  stop  = cumulative_length + length
                  gap(start, stop, count, 'internal')
                end
        cumulative_length += length + 1
        entry
      end
    end
  end
end

#gap(start, stop, count, type) ⇒ Object 



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# File 'lib/genomer-plugin-view/agp.rb', line 58

def gap(start, stop, count, type)
  %W|scaffold #{start} #{stop} #{count} N #{stop - start + 1} scaffold yes #{type}| * "\t"
end

#locations(seq, regex) ⇒ Object 



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# File 'lib/genomer-plugin-view/agp.rb', line 10

def locations(seq,regex)
  seq.upcase.enum_for(:scan, regex).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-view/agp.rb', line 5

def run
  header = "##agp-version	2.0"
  entries.unshift(header).join("\n") + "\n"
end