Class: Bio::Blast::XmlSplitterIterator

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/blast/xmlsplitter.rb

Overview

Reads a full XML result and splits it out into a buffer for each Iteration (query result).

Instance Method Summary collapse

Constructor Details

#initialize(fn) ⇒ XmlSplitterIterator

include Enumerable



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# File 'lib/bio/db/blast/xmlsplitter.rb', line 10

def initialize fn
  @fn = fn
end

Instance Method Details

#to_enum ⇒ Object 



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# File 'lib/bio/db/blast/xmlsplitter.rb', line 14

def to_enum 
  Enumerator.new do | yielder | 
    logger = Bio::Log::LoggerPlus['bio-blastxmlparser']
    logger.info("split file parsing #{@fn}")
    f = File.open(@fn)
    # Skip BLAST header
    f.each_line do | line |
      break if line.strip == "<Iteration>"
    end
    # Return each Iteration as an XML DOM
    each_iteration(f) do | buf |
      iteration = Nokogiri::XML.parse(buf.join) { | cfg | cfg.noblanks }
      yielder.yield NokogiriBlastIterator.new(iteration,self,:prefix=>nil)
    end
  end
end