Module: ViralSeq::Muscle

Defined in:
lib/viral_seq/muscle.rb

Overview

alignment using MUSCLE alignment program

See Also:

Class Method Summary collapse

Class Method Details

.align(ref_seq = "", test_seq = "", algorithm = :PPP, path_to_muscle = false) ⇒ Array

align a sequence with reference sequence Strings

Examples:

seq1 = 'AAGGCGTAGGAC'
seq2 = 'AAGCTTAGGACG'
aligned_seqs = ViralSeq::Muscle.align(seq1,seq2)
=> ["AAGGCGTAGGAC-", "-AAGCTTAGGACG"]

Parameters:

  • ref_seq (String) (defaults to: "") —

    reference sequence

  • test_seq (String) (defaults to: "") —

    test sequence

  • algorithm (Symbol) (defaults to: :PPP) —

    , algorithm for MUSCLE5 only. Choose from :PPP or :Super5.

  • path_to_muscle (String) (defaults to: false) —

    , path to MUSCLE excutable. if not provided (as default), it will use RubyGem::MuscleBio

  • path_to_muscle (String) (defaults to: false) —

    , path to MUSCLE excutable. if not provided (as default), it will use RubyGem::MuscleBio

Returns:

  • (Array) —

    a pair of [:ref_seq_aligned, :test_seq_aligned] or nil if the cannot find MUSCLE excutable



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# File 'lib/viral_seq/muscle.rb', line 42

def self.align(ref_seq = "", test_seq = "", algorithm = :PPP, path_to_muscle = false)
  temp_dir = Dir.home
  temp_name = "_"  + SecureRandom.alphanumeric
  temp_file = File.join(temp_dir, temp_name)
  temp_aln = File.join(temp_dir, (temp_name + "_aln"))
  name = ">test"
  temp_in = File.open(temp_file,"w")
  temp_in.puts ">ref"
  temp_in.puts ref_seq
  temp_in.puts name
  temp_in.puts test_seq
  temp_in.close
  if path_to_muscle
    unless ViralSeq::Muscle.check_muscle?(path_to_muscle)
      File.unlink(temp_file)
      return nil;
    end
    print `#{path_to_muscle} -in #{temp_file} -out #{temp_aln} -quiet`
  else
    if MuscleBio::VERSION.to_f < 0.5
      MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
    else
      MuscleBio.exec(temp_file, temp_aln, algorithm)
    end
  end
  aln_seq_hash = ViralSeq::SeqHash.fa(temp_aln).dna_hash
  File.unlink(temp_file)
  File.unlink(temp_aln)
  return [aln_seq_hash[">ref"], aln_seq_hash[">test"]]
end

.check_muscle?(path_to_muscle) ⇒ boolean

check if path_to_muscle is correct, prompt error messages if MUSCLE is not found.

Parameters:

  • path_to_muscle (String) —

    path to muscle excutable

Returns:

  • (boolean) 


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# File 'lib/viral_seq/muscle.rb', line 11

def self.check_muscle?(path_to_muscle)
  begin
    `#{path_to_muscle} -version`
    return true
  rescue Errno::ENOENT
    puts "
          Error: MUSCLE is not found for at the provided {path_to_muscle}!!
          MUSLCE can be download at http://www.drive5.com/muscle
          Add MUSCLE excutable path to $PATH using
          $  export PATH=$PATH:/path/to/muscle
          or
          provide path_to_MUSCLE in the function arguments\n
          "
    return false
  end
end