module Bio::Big::PhylipReader

Public Class Methods

emit_seq(get_line) { |name, seq| ... } click to toggle source

Define get_line as a lambda function, e.g.

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