Class: Qu::Pcr::Primer3Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/qu/pcr/primer3.rb

Overview

Amplicon

Instance Method Summary collapse

Constructor Details

#initialize(p3_out) ⇒ Primer3Parser 



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# File 'lib/qu/pcr/primer3.rb', line 102

def initialize(p3_out)
  if p3_out.class != String
    $stderr.puts "\tNeed primer3 output file content (not file name) for parsing."
  end
  @p3_out = p3_out
end

Instance Method Details

#records ⇒ Object 



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# File 'lib/qu/pcr/primer3.rb', line 129

def records
  p3_hash = {}
  p3_record = parse
  p3_record.each do |record|
    seq_id = record['SEQUENCE_ID']
    if record.has_key?('PRIMER_ERROR')
      $stderr.puts "\t#{record['PRIMER_ERROR']}"
      return p3_hash
    end
    pp_num = record['PRIMER_PAIR_NUM_RETURNED'].to_i
    if pp_num < 1
      $stderr.puts "\tFailed design for %s" % [seq_id]
      $stderr.puts "\tLeft: #{record['PRIMER_LEFT_EXPLAIN']}"
      $stderr.puts "\tRight: #{record['PRIMER_RIGHT_EXPLAIN']}"
      $stderr.puts "\INTERNAL: #{record['PRIMER_INTERNAL_EXPLAIN']}" if record.has_key?("PRIMER_INTERNAL_EXPLAIN")
      $stderr.puts "\tPair: #{record['PRIMER_PAIR_EXPLAIN']}"
    end
    p3_hash[seq_id] = []
    (0...pp_num).each do |i|
      p3_hash[seq_id] << Amplicon.new(record, i, type='primer3')
    end
  end

  return p3_hash
end