Module: Bio::Big::PhylipReader

Defined in:
lib/bigbio/db/phylip.rb

Class Method Summary collapse

Class Method Details

.emit_seq(get_line) ⇒ Object

Define get_line as a lambda function, e.g.

Bio::Big::PhylipReader.emit_seq(-> { lines.next }) { | name, seq | p [name,seq] }



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# File 'lib/bigbio/db/phylip.rb', line 22

def PhylipReader::emit_seq get_line
  line = get_line.call.strip
  a = line.split
  seq_num = a[0].to_i
  seq_size = a[1].to_i
  name = nil
  seq = ""
  while true
    line = get_line.call
    break if line == nil or line == ""
    line = line.strip
    if name == nil
      name = line
      next
    end
    seq += line
    if seq.size >= seq_size
      raise "Name wrong size for #{name}" if name.size > 20
      raise "Sequence wrong size for #{name}" if seq.size > seq_size
      yield name, seq
      name = nil
      seq = ""
    end
  end
end