Module: Ms::Ident

Defined in:
lib/ms/ident.rb

Constant Summary collapse

IPI_RE = 
/IPI:([\w\d\.]+)\|/
GI_RE = 
/gi|([\w\d\.]+)\|/
STANDARD_AA =

the twenty standard amino acids

%w(A C D E F G H I K L M N P Q R S T V W Y)
DEFAULT_PEPTIDE_CENTRIC_DB = 
{:missed_cleavages => 1, :min_length => 8, :enzyme => Ms::InSilico::Digester::TRYPSIN, :id_regexp => nil, :remove_digestion_file => true, :cleave_initiator_methionine => true, :expand_aa => {'X' => STANDARD_AA}}

Class Method Summary collapse

Class Method Details

.expand_peptides(peptide, expand_aa) ⇒ Object

does combinatorial expansion of all letters requesting it. expand_aa is hash like: ‘X’=>STANDARD_AA



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# File 'lib/ms/ident.rb', line 105

def self.expand_peptides(peptide, expand_aa)
  letters_in_order = expand_aa.keys.sort
  index_and_key = []
  peptide.split('').each_with_index do |char,i| 
    if let_index = letters_in_order.index(char) 
      index_and_key << [i, letters_in_order[let_index]]
    end
  end
  to_expand = [peptide]
  index_and_key.each do |i,letter|
    new_peps = []
    while current_pep = to_expand.shift do
      new_peps << expand_aa[letter].map {|v| dp = current_pep.dup ; dp[i] = v ; dp }
    end
    to_expand = new_peps.flatten
  end
  to_expand
end

.peptide_centric_db(fasta_file, opts = {}) ⇒ Object

writes a new file with the added ‘min_aaseq<Integer>’ creates a temporary digestion file that contains all peptides digesting with certain missed_cleavages (i.e., min_seq_length is not applied to this file but on the final peptide centric db)



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# File 'lib/ms/ident.rb', line 19

def self.peptide_centric_db(fasta_file, opts={})
  opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)

  (missed_cleavages, min_length, enzyme, id_regexp, remove_digestion_file, cleave_initiator_methionine, expand_aa) = opts.values_at(:missed_cleavages, :min_length, :enzyme, :id_regexp, :remove_digestion_file, :cleave_initiator_methionine, :expand_aa) 

  unless id_regexp
    id_regexp = Ms::Fasta.id_regexp(Ms::Fasta.filetype(fasta_file))
    raise RuntimeError, "fasta file type not recognized, supply id_regexp" unless id_regexp
  end

  start_time = Time.now
  print "Digesting #{fasta_file} ..." if $VERBOSE

  if expand_aa
    letters_to_expand_re = Regexp.new("[" << Regexp.escape(expand_aa.keys.join) << "]")
  end

  base = fasta_file.chomp(File.extname(fasta_file))
  digestion_file = base + ".msd_clvg#{missed_cleavages}.peptides"
  File.open(digestion_file, "w") do |fh|
    Ms::Fasta.open(fasta_file) do |fasta|
      fasta.each do |prot|
        peptides = enzyme.digest(prot.sequence, missed_cleavages)
        if (cleave_initiator_methionine && (prot.sequence[0,1] == "M"))
          m_peps = []
          init_methionine_peps = []
          peptides.each do |pep|
            # if the peptide is at the beginning of the protein sequence
            if prot.sequence[0,pep.size] == pep
              m_peps << pep[1..-1]
            end
          end
          peptides.push(*m_peps)
        end
        if expand_aa
          peptides = peptides.map do |pep|
            if pep =~ letters_to_expand_re
              expand_peptides(pep, expand_aa)
            else
              pep
            end
          end.flatten
        end
        fh.puts( prot.header.split(/\s+/).first + "\t" + peptides.join(" ") )
      end
    end
  end
  puts "#{Time.now - start_time} sec" if $VERBOSE

  
  start_time = Time.now
  print "Organizing raw digestion #{digestion_file} ..." if $VERBOSE

  hash = Hash.new {|h,k| h[k] = [] }
  IO.foreach(digestion_file) do |line|
    (prot, *peps) = line.chomp!.split(/\s+/)
    id = prot.match(id_regexp)[1]
    peps.each do |pep|
      if pep.size >= min_length
        hash[pep] << id
      end
    end
  end
  puts "#{Time.now - start_time} sec" if $VERBOSE

  base = digestion_file.chomp(File.extname(digestion_file))
  final_outfile = base + ".min_aaseq#{min_length}" + ".yml"

  start_time = Time.now
  print "Writing results to #{} ..." if $VERBOSE

  File.open(final_outfile, 'w') do |out|
    hash.each do |k,v|
      out.puts( "#{k}: #{v.join('-')}" )
    end
  end
  puts "#{Time.now - start_time} sec" if $VERBOSE

  if remove_digestion_file
    File.unlink(digestion_file)
  end

end