module Bio::BioAlignment::DelShortSequences

Public Instance Methods

del_short_sequences(percentage=30) click to toggle source

Return an alignment with the bridges removed

# File lib/bio-alignment/edit/del_short_sequences.rb, line 23
def del_short_sequences percentage=30
  mark_short_sequences.rows_where { |row| !row.state.deleted? }
end
mark_short_sequences(percentage = 30) click to toggle source

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

# File lib/bio-alignment/edit/del_short_sequences.rb, line 12
def mark_short_sequences percentage = 30
  mark_rows { |state,row| 
    num = row.count { |e| e.gap? }
    if (num.to_f/row.length) > 1.0-percentage/100.0
      state.delete!
    end
    state
  }
end