module Bio::BioAlignment::DelNonInformativeSequences
Public Instance Methods
del_non_informative_sequences(percentage=30)
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# File lib/bio-alignment/edit/del_non_informative_sequences.rb, line 26 def del_non_informative_sequences percentage=30 mark_non_informative_sequences(percentage).rows_where { |row| !row.state.deleted? } end
mark_non_informative_sequences(percentage = 30)
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Count the informative elements in a sequence. If the count is less than percentage
mark the sequence for deletion.
Return a new alignment with rows marked for deletion, i.e. mark rows that mostly contain undefined elements and gaps (threshold percentage
). The alignment returned is a cloned copy
# File lib/bio-alignment/edit/del_non_informative_sequences.rb, line 15 def mark_non_informative_sequences percentage = 30 percentage=30 if not percentage # for CLI mark_rows { |state,row| num = row.count { |e| e.gap? or e.undefined? } if (num.to_f/row.length) > 1.0-percentage/100.0 state.delete! end state } end