mspire 0.4.9 → 0.5.0

data/lib/spec_id/sequest/params.rb

@@ -1,316 +0,0 @@
-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
-