mspire 0.2.4 → 0.3.0

data/lib/spec_id/sequest/params.rb

@@ -0,0 +1,316 @@
+require 'sample_enzyme'
+
+
+##
+# In the future, this guy should accept any version of bioworks params file
+# and spit out any param queried.
+module Sequest ; end
+class Sequest::Params
+
+  Bioworks31_Enzyme_Info_Array = [
+    ['No_Enzyme', 0, '-', '-'],   # 0
+    ['Trypsin', 1, 'KR', '-'],  # 1
+    ['Trypsin(KRLNH)', 1, 'KRLNH', '-'],  # 2
+    ['Chymotrypsin', 1, 'FWYL', '-'],  # 3
+    ['Chymotrypsin(FWY)', 1, 'FWY', 'P'],  # 4
+    ['Clostripain', 1, 'R', '-'],  # 5
+    ['Cyanogen_Bromide', 1, 'M', '-'],  # 6
+    ['IodosoBenzoate', 1, 'W', '-'],  # 7
+    ['Proline_Endopept', 1, 'P', '-'],  # 8
+    ['Staph_Protease', 1, 'E', '-'],  # 9
+    ['Trypsin_K', 1, 'K', 'P'],  # 10
+    ['Trypsin_R', 1, 'R', 'P'],  # 11
+    ['GluC', 1, 'ED', '-'],  # 12
+    ['LysC', 1, 'K', '-'],  # 13
+    ['AspN', 0, 'D', '-'],  # 14
+    ['Elastase', 1, 'ALIV', 'P'],  # 15
+    ['Elastase/Tryp/Chymo', 1, 'ALIVKRWFY', 'P'],  # 16
+  ]
+
+  # current attributes supported are:
+  # bioworks 3.2:
+  @@param_re = / = ?/o
+  @@param_two_split = ';'
+  @@sequest_line = /\[SEQUEST\]/o
+
+  # the general options
+  attr_accessor :opts
+  # the static weights added to amino acids
+  attr_accessor :mods
+
+  # all keys and values stored as strings!
+  # will accept a sequest.params file or .srf file
+  def initialize(file=nil)
+    if file
+      parse(file)
+    end
+  end
+
+  # returns hash of params up until add_U_user_amino_acid
+  def grab_params(fh)
+    hash = {}
+    in_add_amino_acid_section = false
+    add_section_re = /^\s*add_/
+    prev_pos = nil
+    while line = fh.gets
+      if line =~ add_section_re
+        in_add_amino_acid_section = true
+      end
+      if (in_add_amino_acid_section and !(line =~ add_section_re))
+        fh.pos = prev_pos
+        break
+      end
+      prev_pos = fh.pos
+      if line =~ /\w+/
+        one,two = line.split @@param_re
+        two,comment = two.split @@param_two_split
+        hash[one] = two.rstrip
+      end
+    end
+    hash
+  end
+
+  # returns self
+  def parse_handle(fh)
+    # seek to the SEQUEST file
+    loop do
+      if fh.gets =~ @@sequest_line
+        # double check that we are in a sequest params file:
+        pos = fh.pos
+        if fh.gets =~ /^first_database_name/
+          fh.pos = pos
+          break
+        end
+      end
+    end
+    @opts = grab_params(fh)
+    @opts["search_engine"] = "SEQUEST"
+    # extract out the mods
+    @mods = {}
+    @opts.each do |k,v|
+      if k =~ /^add_/
+        @mods[k] = @opts.delete(k)
+      end
+    end
+
+    ## this gets rid of the .hdr postfix on indexed databases
+    @opts["first_database_name"] = @opts["first_database_name"].sub(/\.hdr$/, '')
+    self
+  end
+
+  ## parses file
+  ## and drops the .hdr behind indexed fasta files
+  ## returns self
+  ## can read sequest.params file or .srf file handle
+  def parse(file)
+    File.open(file) do |fh|
+      parse_handle(fh)
+    end
+    self
+  end
+
+  # returns( offset, cleave_at, except_if_after )
+  # offset is an Integer specifying how far after an amino acid to cut
+  # cleave_at is a string of all amino acids that should be cut at
+  # except_if_after for not cutting after those
+  # normal tryptic behavior would be: [1, 'KR', 'P']
+  # NOTE: a '-' in a params file is returned as an '' (empty string)
+  # AspN is [0,'D','']
+  def enzyme_specificity
+    enzyme_ar = 
+      if version == '3.1'
+        Bioworks31_Enzyme_Info_Array[@opts['enzyme_number'].to_i][1,3]
+      elsif version >= '3.2'
+        arr = enzyme_info.split(/\s+/)[2,3]
+        arr[0] = arr[0].to_i
+        arr
+      else
+        raise ArgumentError, "don't recognize anything but Bioworks 3.1--3.3"
+      end
+    enzyme_ar.map! do |str|
+      if str == '-' ; ''
+      else ; str
+      end
+    end
+    enzyme_ar
+  end
+
+  # Returns the version of the sequest.params file
+  # Returns String "3.3" if contains "fragment_ion_units"
+  # Returns String "3.2" if contains "enyzme_info"
+  # Returns String "3.1" if contains "enzyme_number"
+  def version
+    if @opts['fragment_ion_units'] ; return '3.3'
+    elsif @opts['enzyme_info'] ; return '3.2'
+    elsif @opts['enzyme_number'] ; return '3.1'
+    end
+  end
+
+  ####################################################
+  # TO PEPXML
+  ####################################################
+  # In some ways, this is merely translating to the older Bioworks
+  # sequest.params files
+
+  # I'm not sure if this is the right mapping for sequence_search_constraint?
+  def sequence
+    pseq = @opts['partial_sequence'] 
+    if !pseq || pseq == "" ; pseq = "0" end
+    pseq
+  end
+
+  def precursor_mass_type
+    case @opts['mass_type_parent']
+    when '0' ; "average" 
+    when '1' ; "monoisotopic"
+    else ; abort "error in mass_type_parent in sequest!"
+    end
+  end
+
+  def fragment_mass_type
+    fmtype = 
+      case @opts['mass_type_fragment']
+      when '0' ; "average"
+      when '1' ; "monoisotopic"
+      else ; abort "error in mass_type_fragment in sequest!"
+      end
+  end
+
+  def method_missing(name, *args)
+    string = name.to_s
+    if @opts.key?(string)    ; return @opts[string]
+    elsif @mods.key?(string) ; return @mods[string]
+    else                     ; return nil
+    end
+  end
+
+  ## We only need to define values if they are different than sequest.params
+  ## The method_missing will look them up in the hash!
+
+  # Returns a system independent basename
+  # Splits on "\" or "/"
+  def _sys_ind_basename(file)
+    return file.split(/[\\\/]/)[-1]
+  end
+
+  # changes the path of the database
+  def database_path=(newpath)
+    db = @opts["first_database_name"]
+    newpath = File.join(newpath, _sys_ind_basename(db))
+    @opts["first_database_name"] = newpath
+  end
+
+  def database
+    @opts["first_database_name"]
+  end
+
+  # returns the appropriate aminoacid mass lookup table (in spec_id.rb SpecID::MONO or
+  # SpecID::AVG based on precursor_mass_type
+  def mass_table
+    case precursor_mass_type
+    when 'average'
+      SpecID::AVG
+    when 'monoisotopic'
+      SpecID::MONO
+    end
+  end
+
+  # at least in Bioworks 3.2, the First number after the enzyme
+  # is the indication of the enzymatic end stringency (required):
+  #   1 = Fully enzymatic
+  #   2 = Either end
+  #   3 = N terminal only
+  #   4 = C terminal only
+  # So, to get min_number_termini we map like this:
+  #   1 => 2
+  #   2 => 1
+  def min_number_termini
+    termini_number = @opts["enzyme_info"].split(" ")[1]
+    if termini_number == "1"
+      return "2"
+    elsif termini_number == "2"
+      return "1"
+    else
+      puts "WARNING: Enzyme termini info might be imprecise!"
+      return "1"
+    end
+  end
+
+  # returns a SampleEnzyme object
+  def sample_enzyme
+    (offset, cleave_at, except_if_after) = enzyme_specificity.map do |v|
+      if v == '' ; nil ; else v end
+    end
+    SampleEnzyme.new do |se|
+      se.name = self.enzyme
+      se.cut = cleave_at
+      se.no_cut = except_if_after
+      se.sense =
+        if se.name == "No_Enzyme"
+          nil
+        elsif offset == 1
+          'C'
+        elsif offset == 0
+          'N'
+        end
+    end
+  end
+
+  # returns the enzyme name (but no parentheses connected with the name).
+  # this will likely be capitalized.
+  def enzyme
+    v = self.version
+    basic_name = 
+      if v == '3.1'
+        Bioworks31_Enzyme_Info_Array[ @opts['enzyme_number'].to_i ][0]
+      elsif v >= '3.2'
+        @opts["enzyme_info"]
+      end
+    basic_name.split('(')[0]
+  end
+
+  def max_num_internal_cleavages
+    @opts["max_num_internal_cleavage_sites"]
+  end
+
+  # my take on peptide_mass_units:
+  # (see http://www.ionsource.com/tutorial/isotopes/slide2.htm)
+  # amu = atomic mass units = (mass_real - mass_measured).abs (??abs??)
+  # mmu = milli mass units (amu / 1000)
+  # ppm = parts per million = 10^6 * ∆m_accuracy / mass_measured  [ where ∆m_accuracy = mass_real – mass_measured ]
+
+  def peptide_mass_tol
+    if @opts["peptide_mass_units"] != "0"
+      puts "WARNING: peptide_mass_tol units need to be adjusted!"
+    end
+    @opts["peptide_mass_tolerance"]
+  end
+
+  def fragment_ion_tol
+    @opts["fragment_ion_tolerance"]
+  end
+
+  def max_num_differential_AA_per_mod
+    @opts["max_num_differential_per_peptide"]
+  end
+
+  # returns a hash by add_<whatever> of any static mods != 0
+  # the values are still as strings
+  def static_mods
+    hash = {}
+    @mods.each do |k,v|
+      if v.to_f != 0.0
+        hash[k] = v
+      end
+    end
+    hash
+  end
+
+  ## @TODO: We could add some of the parameters not currently being asked for to be more complete
+  ## @TODO: We could always add the Bioworks 3.2 specific params as params
+
+  ####################################################
+  ####################################################
+
+end
+