Class: Mspire::Ident::Peptide::Db::Creator

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/ident/peptide/db/creator.rb

Constant Summary collapse

MAX_NUM_AA_EXPANSION = 
3
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)
EXPAND_AA = 
{'X' => STANDARD_AA}
DEFAULT_PEPTIDE_CENTRIC_DB = 
{
  missed_cleavages: 2, 
  min_length: 5,
  enzyme: Mspire::Digester[:trypsin], 
  remove_digestion_file: true, 
  cleave_initiator_methionine: true, 
  expand_aa: false, 
  uniprot: true,
  data_type: :hash,
}

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.cmdline(argv) ⇒ Object

sets defaults according to DEFAULT_PEPTIDE_CENTRIC_DB



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 25

def self.cmdline(argv)
  opt = DEFAULT_PEPTIDE_CENTRIC_DB.dup

  opts = OptionParser.new do |op|
    op.banner = "usage: #{File.basename($0)} <file>.fasta ..."
    op.separator "output: "
    op.separator "    <file>.msd_clvg<missed_cleavages>.min_aaseq<min_length>.yml"
    op.separator "format:"
    op.separator "    PEPTIDE: ID1<tab>ID2<tab>ID3..."
    op.separator ""    
    op.separator "    Initiator Methionines - by default, will generate two peptides"
    op.separator "    for any peptide found at the N-termini starting with 'M'"
    op.separator "    (i.e., one with and one without the leading methionine)"
    op.separator ""
    op.on("--missed-cleavages <#{opt[:missed_cleavages]}>", Integer, "max num of missed cleavages") {|v| opt[:missed_cleavages] = v }
    op.on("--min-length <#{opt[:min_length]}>", Integer, "the minimum peptide aaseq length") {|v| opt[:min_length] = v }
    op.on("--no-cleaved-methionine", "does not cleave off initiator methionine") { opt[:cleave_initiator_methionine] = false }
    op.on("--expand-x", "enumerate all aa possibilities for 'X'", "(default is to remove these peptides)") {|v| opt[:expand_aa] = v }
    op.on("--no-uniprot", "use entire protid section of fasta header", "for non-uniprot fasta files") { opt[:uniprot] = false }
    #op.on("--trie", "use a trie (for very large uniprot files)", "must have fast_trie gem installed") {|v| opt[:trie] = v }
    op.on("--data-type <#{opt[:data_type]}>", "hash|google_hash|trie", "need google_hash or fast_trie gem installed") {|v| opt[:data_type] = v.to_sym }

    op.on("-e", "--enzyme <#{opt[:enzyme].name}>", "enzyme for digestion (Mspire::Digester[name])") {|v| opt[:enzyme] = Mspire::Digester[v] }
    op.on("-v", "--verbose", "talk about it") { $VERBOSE = 5 }
    op.on("--list-enzymes", "lists approved enzymes and exits") do
    op.on("-v", "--verbose", "talk about it") { $VERBOSE = 5 }
      puts Mspire::Digester::ENZYMES.keys.join("\n")
      exit
    end
  end

  opts.parse!(argv)

  if argv.size == 0
    puts opts || exit
  end

  argv.map do |file|
    creator = Mspire::Ident::Peptide::Db::Creator.new
    creator.create(file, opt)
  end
end

Instance Method Details

#create(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) returns the full name of the written file.



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 223

def create(fasta_file, opts={})
  opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)
  digestion_file = create_digestion_file(fasta_file, opts)
  puts "created file of size: #{File.size(digestion_file)}" if $VERBOSE
  db_from_fasta_digestion_file(digestion_file, opts)
end

#create_digestion_file(fasta_file, opts = {}) ⇒ Object

returns the name of the digestion file that was written



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 69

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

  (missed_cleavages, enzyme, cleave_initiator_methionine, expand_aa) = opts.values_at(:missed_cleavages, :enzyme, :cleave_initiator_methionine, :expand_aa) 
  start_time = Time.now
  print "Digesting #{fasta_file} ..." if $VERBOSE

  letters_to_expand_re = Regexp.new("[" << Regexp.escape(EXPAND_AA.keys.join) << "]")

  base = fasta_file.chomp(File.extname(fasta_file))
  digestion_file = base + ".msd_clvg#{missed_cleavages}.peptides"
  File.open(digestion_file, "w") do |fh|
    Mspire::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
        peptides = 
          if expand_aa
            peptides.flat_map do |pep|
              (pep =~ letters_to_expand_re) ? expand_peptides(pep, EXPAND_AA) : pep
            end
          else
            peptides.select {|pep| pep !~ letters_to_expand_re }
          end
        header = prot.header
        id = opts[:uniprot] ? Mspire::Fasta.uniprot_id(header) : header.split(/\s/,2).first
        fh.puts( id + "\t" + peptides.join(" ") )
      end
    end
  end
  puts "#{Time.now - start_time} sec" if $VERBOSE
  digestion_file
end

#db_from_fasta_digestion_file(digestion_file, opts = {}) ⇒ Object

returns the full path of the created file



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 114

def db_from_fasta_digestion_file(digestion_file, opts={})
  opts = DEFAULT_PEPTIDE_CENTRIC_DB.merge(opts)

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

  puts "#{Time.now - start_time} sec" if $VERBOSE
  hash_like = hash_like_from_digestion_file(digestion_file, opts[:min_length], opts[:data_type])

  base = digestion_file.chomp(File.extname(digestion_file))
  final_outfile = 
    if opts[:data_type] == :trie
      base + ".min_aaseq#{opts[:min_length]}"
    else
      base + ".min_aaseq#{opts[:min_length]}" + ".yml"
    end

  start_time = Time.now
  print "Writing #{hash_like.size} peptides to #{} ..." if $VERBOSE

    if opts[:data_type] == :trie
      trie = hash_like
      trie.save(final_outfile)
    else
      File.open(final_outfile, 'w') do |out|
      hash_like.each do |k,v|
        out.puts( [k, v.join(Mspire::Ident::Peptide::Db::PROTEIN_DELIMITER)].join(Mspire::Ident::Peptide::Db::KEY_VALUE_DELIMITER) )
        #out.puts "#{k}#{Mspire::Ident::Peptide::Db::KEY_VALUE_DELIMITER}#{v}"       
      end
    end
  end
  puts "#{Time.now - start_time} sec" if $VERBOSE

  if opts[:remove_digestion_file]
    File.unlink(digestion_file)
  end
  File.expand_path(final_outfile)
end

#expand_peptides(peptide, expand_aa_hash) ⇒ Object

does combinatorial expansion of all letters requesting it. expand_aa is hash like: ‘X’=>STANDARD_AA returns nil if there are more than MAX_NUM_AA_EXPANSION amino acids to be expanded returns an empty array if there is no expansion



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 235

def expand_peptides(peptide, expand_aa_hash)
  letters_in_order = expand_aa_hash.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
  if index_and_key.size > MAX_NUM_AA_EXPANSION
    return nil
  end
  to_expand = [peptide]
  index_and_key.each do |i,letter|
    new_peps = []
    while current_pep = to_expand.shift do
      new_peps << expand_aa_hash[letter].map {|v| dp = current_pep.dup ; dp[i] = v ; dp }
    end
    to_expand = new_peps.flatten
  end
  to_expand
end

#get_a_trie ⇒ Object 



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 153

def get_a_trie
  begin
    require 'trie'
  rescue
    raise LoadError, "must first install fast_trie"
  end
  Trie.new
end

#hash_like_from_digestion_file(digestion_file, min_length, data_type = :hash) ⇒ Object

data_type can be :hash (default), :google_hash (better memory and speed), or :trie (experimental/broken)



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# File 'lib/mspire/ident/peptide/db/creator.rb', line 164

def hash_like_from_digestion_file(digestion_file, min_length, data_type=:hash)
  case data_type
  when :trie
    trie = get_a_trie
    ::IO.foreach(digestion_file) do |line|
      line.chomp!
      (prot, *peps) = line.split(/\s+/)
      # prot is something like this: "P31946"
      peps.uniq!
      peps.each do |pep|
        if pep.size >= min_length
          if trie.has_key?(pep)
            ar = trie.get(pep)
            ar << prot
          else
            trie.add( pep, [prot] )
          end
        end
      end
    end
    trie
  when :hash, :google_hash
    hash = 
      case data_type
      when :hash
        Hash.new
      when :google_hash
        require 'google_hash'
        # this guy is very slow compared to ruby hash (10X slower?) but more
        # memory efficient (but only ~10% or so improvement with this
        # application)
        GoogleHashDenseRubyToRuby.new
        # still need to try Sparse one out and compare performance
        #GoogleHashSparseRubyToRuby.new
      end
    ::IO.foreach(digestion_file) do |line|
      line.chomp!
      (prot, *peps) = line.split(/\s+/)
      # prot is something like this: "P31946"
      peps.uniq!
      peps.each do |pep|
        if pep.size >= min_length
          if hash.key?(pep)
            hash[pep] << prot
          else
            hash[pep] = [prot]
          end
        end
      end
    end
    hash
  end
end