Module: Qu::Utils

Defined in:
lib/qu/utils.rb,
lib/qu/utils/version.rb

Constant Summary collapse

IUPAC = 
{
  A: ['A'],
  T: ['T'],
  C: ['C'],
  G: ['G'],
  R: ['G', 'A'],
  Y: ['T', 'C'],
  S: ['G', 'C'],
  W: ['T', 'A'],
  K: ['G', 'T'],
  M: ['A', 'C'],
  D: ['G', 'T', 'A'],
  H: ['T', 'A', 'C'],
  B: ['G', 'T', 'C'],
  V: ['G', 'A', 'C'],
  N: ['G', 'A', 'T', 'C'],
  I: ['G', 'A', 'T', 'C'],
}
VERSION = 
"1.0.3"

Class Method Summary collapse

Class Method Details

.convert_degenerate_primer(primer_file) ⇒ Object 



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# File 'lib/qu/utils.rb', line 45

def convert_degenerate_primer(primer_file)
  primer_records = Bio::FlatFile.new(Bio::FastaFormat, File.open(primer_file))

  primer_list = []
  primer_records.each do |primer|
    if primer.naseq.to_s =~ /[^atcgATCG]+/
      normal_seq_list = iupac2normal(primer.naseq.upcase)
      fasta_io = StringIO.new
      normal_seq_list.each_with_index do |normal_seq, index|
        fasta_io << ">#{primer.entry_name}_#{index+1} #{primer.description}\n#{normal_seq}\n"
      end
      fasta_io.rewind
      primer_list += Bio::FlatFile.new(Bio::FastaFormat, fasta_io).to_a
      fasta_io.close
    else
      primer_list << primer
    end
  end

  return primer_list
end

.iupac2normal(seq, prefixes = ['']) ⇒ Object 



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# File 'lib/qu/utils.rb', line 28

def iupac2normal(seq, prefixes = [''])
  return prefixes if seq.size == 0

  first = seq[0].to_sym
  last_seq = seq[1..-1]
  new_prefixes = []
  prefixes.each do |prefix|
    if IUPAC.include?(first)
      IUPAC[first].each {|base| new_prefixes << "#{prefix}#{base}"}
    else
      $stderr.puts "Error: unrecognized base: #{first}"
      exit
    end
  end
  return iupac2normal(last_seq, prefixes = new_prefixes)
end

.long_seq_wrap(word, length = 80, separator = "\n") ⇒ Object 



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# File 'lib/qu/utils.rb', line 74

def long_seq_wrap(word, length=80, separator="\n")
  # Wrap a long sentence with may words into multiple lines
  (word.length < length) ?
    word :
    word.scan(/.{1,#{length}}/).join(separator)
end

.platform_bit ⇒ Object 



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# File 'lib/qu/utils.rb', line 112

def platform_bit
  OS.bits
end

.platform_os ⇒ Object 



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# File 'lib/qu/utils.rb', line 100

def platform_os
  if OS.windows?
    return 'windows'
  elsif OS.mac?
    return 'mac'
  elsif OS.linux?
    return 'linux'
  else
    return 'unknown'
  end
end

.plural_word(word, count) ⇒ Object 



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# File 'lib/qu/utils.rb', line 96

def plural_word(word, count)
  count > 1 ? word + 's' : word
end

.seconds_to_units(seconds) ⇒ Object 



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# File 'lib/qu/utils.rb', line 81

def seconds_to_units(seconds)
  return "#{seconds.round(2)} second" if seconds < 1
  return "#{seconds.round(2)} seconds" if seconds < 60
  '%d minutes, %d seconds' %
  #'%d days, %d hours, %d minutes, %d seconds' %
  # the .reverse lets us put the larger units first for readability

  #[24,60,60].reverse.inject([seconds]) {|result, unitsize|

  [60].reverse.inject([seconds]) {|result, unitsize|
    result[0,0] = result.shift.divmod(unitsize)
    result
  }
end

.word_wrap(text, line_width = 80) ⇒ Object

File actionpack/lib/action_view/helpers/text_helper.rb, line 215



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# File 'lib/qu/utils.rb', line 68

def word_wrap(text, line_width = 80)
  text.split("\n").collect do |line|
    line.length > line_width ? line.gsub(/(.{1,#{line_width}})(\s+|$)/, "\\1\n").strip : line
  end * "\n"
end