Module: Bio::BioAlignment::DelBridges

Includes:
MarkColumns
Defined in:
lib/bio-alignment/edit/del_bridges.rb

Instance Method Summary collapse

Methods included from MarkColumns

#mark_columns

Instance Method Details

#del_bridges(percentage = 30) ⇒ Object

Return an alignment with the bridges removed



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# 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) ⇒ Object

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



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# 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