module Bio::BioAlignment::DelBridges

Public Instance Methods

del_bridges(percentage=30) click to toggle source

Return an alignment with the bridges removed

# File lib/bio-alignment/edit/del_bridges.rb, line 23
def del_bridges percentage=30
  mark_bridges.columns_where { |col| !col.state.deleted? }
end
mark_bridges(percentage = 30) click to toggle source

Return a new alignment with columns marked for deletion, i.e. mark columns that mostly contain gaps (threshold percentage). The alignment returned is a cloned copy

# File lib/bio-alignment/edit/del_bridges.rb, line 12
def mark_bridges percentage = 30
  mark_columns { |state,column| 
    num = column.count { |e| e.gap? or e.undefined? }
    if (num.to_f/column.length) > 1.0-percentage/100.0
      state.delete!
    end
    state
  }
end