Module: Bio::BioAlignment::MaskIslands

Includes:
MarkRows
Defined in:
lib/bio-alignment/edit/mask_islands.rb

Defined Under Namespace

Classes: IslandElementState

Instance Method Summary collapse

Methods included from MarkRows

#mark_row_elements, #mark_rows

Instance Method Details

#mark_islands ⇒ Object

Drop all ‘islands’ in a sequence with low consensus, that show a gap larger than ‘min_gap_size’ (default 3) on both sides, and are shorter than ‘max_island_size’ (default 30). An island larger than 30 elements is arguably no longer an island, and low consensus stretches may be loops - it is up to the alignment procedure to get that right. We also allow for micro deletions inside an alignment (1 or 2 elements). The island consensus is calculated by column. If more than 50% of the island shows consensus, the island is retained. Consensus for each element is defined as the number of matches in the column (default 1).



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# File 'lib/bio-alignment/edit/mask_islands.rb', line 25

def mark_islands
  mark_row_elements { |row,rownum|
    # first set state and find unique elements (i.e. consensus)
    row.each_with_index do |e,colnum|
      e.state = IslandElementState.new
      column = columns[colnum]
      e.state.unique = (column.count{|e2| !e2.gap? and e2 == e } == 1)
      # p [e,e.state,e.state.unique]
    end
    # group elements into islands (split on gap) and mask
    gap = []
    island = []
    in_island = true
    row.each do |e|
      if not in_island
        if e.gap?
          gap << e
        else
          island << e
          in_island = true
          gap = []
        end
      else # in_island
        if not e.gap?
          island << e
          gap = []
        else
          gap << e
          if gap.length > 2
            in_island = false
            mark_island(island)
            # print_island(island)
            island = []
          end
        end
      end
    end
    if in_island
      mark_island(island)
      # print_island(island) if island.length > 0
    end
    # row.each_with_index do |e,colnum|
    #   e.state = ElementState.new
    #   column = columns[colnum]
    #   e.state.mask! if column.count{|e2| !e2.gap? and e2 == e } == 1
    #   # print e,',',e.state,';'
    # end
    # now make sure there are at least 5 in a row, otherwise
    # start unmasking. First group all elements
    # group = []
    # row.each_with_index do |e,colnum|
    #   next if e.gap?
    #   if e.state.masked?
    #     group << e
    #   else
    #     if group.length <= min_serial
    #       # the group is too small
    #       group.each do | e2 |
    #         e2.state.unmask!
    #       end
    #     end
    #     group = []
    #   end
    # end
    row  # return changed sequence
  }
end