mspire-mascot-dat 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/LICENSE.txt

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+Copyright (c) 2013 Brigham Young University
+Authored by: John T. Prince
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# mspire-mascot-dat
+
+Reads the mascot search engine .dat results file.
+
+## Examples
+
+```ruby
+require 'mspire-mascot-dat'
+
+Mspire::Mascot::Dat.open(file.dat) do |dat|
+  dat.sections  # => [:parameters, :masses, :unimod, :enzyme ...]
+end
+
+```
+### each peptide
+
+#### every peptide hit
+
+```ruby
+dat.each_peptide do |pephit|
+  pephit.missed_cleavages # => an Integer
+  pephit.ions_score # => a Float
+  ...
+end
+```
+
+#### every decoy peptide hit
+
+```ruby
+dat.each_peptide(false) {|pephit| ... }
+```
+
+#### each top peptide hit
+
+```ruby
+dat.each_peptide(true, 1) {|pephit| ... }
+```
+
+## Further Info
+
+See Mascot's Installation & Setup Manual' for detailed information about the
+.dat format itself.
+
+## Copyright
+
+MIT.  See LICENSE.txt

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "mspire-mascot-dat"
+  gem.homepage = "http://github.com/princelab/mspire-mascot-dat"
+  gem.license = "MIT"
+  gem.summary = %Q{Reads mascot dat files for mspire library.}
+  gem.description = %Q{Reads mascot dat files with gusto for mspire library.}
+  gem.email = "jtprince@gmail.com"
+  gem.authors = ["John T. Prince"]
+  gem.add_dependency "elif", "~> 0.1.0"
+  gem.add_development_dependency "rspec", "~> 2.8.0"
+  gem.add_development_dependency "rdoc", "~> 3.12"
+  gem.add_development_dependency "jeweler", "~> 1.8.4"
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "mspire-mascot-dat #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/mspire/mascot/dat/index.rb

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+require 'elif'
+
+module Mspire
+  module Mascot
+    class Dat
+      # makes a byte index (not line index) 
+      class Index
+
+        # the hash holding the start byte for each section (besides the
+        # queries)
+        attr_accessor :byte_num
+
+        # the array holding the start byte for each query.  It is indexed by
+        # query number, so the first 
+        attr_accessor :query_num_to_byte
+
+        # an array of the query nums
+        attr_accessor :query_nums
+
+        def initialize(io=nil)
+          @byte_num = {}
+          @query_num_to_byte = []
+          @query_nums = []
+          from_io(io) if io
+        end
+
+        def has_queries?
+          @query_nums.size > 0
+        end
+
+        # returns self
+        def from_io(io)
+          io.rewind
+          while line=io.gets
+            io.each_line do |line|
+              if md=/^Content-Type: application\/x-Mascot; name=["'](\w+)["']/.match(line)
+                head = md[1]
+                io.gets # the newline
+                pos = io.pos
+
+                if qmd=/query(\d+)/.match(head)
+                  query_num = qmd[1].to_i
+                  @query_nums << query_num                
+                  @query_num_to_byte[query_num] = pos
+                else
+                  @byte_num[head] = pos
+                end
+              end
+            end
+          end
+          io.rewind
+
+          @query_nums.freeze
+          @query_num_to_byte.freeze
+          @byte_num.freeze
+          self
+        end
+
+        # given a string or symbol, looks up the start line.  Given an
+        # Integer, assumes it is a query num and returns the start line of the
+        # query number.
+        def [](key)
+          if key.is_a?(Integer) 
+            @query_num_to_byte[key]
+          else
+            @byte_num[key.to_s]
+          end
+        end
+
+        # nil if the query is out of bounds
+        def query(n)
+          @query_num_to_byte[n]
+        end
+
+      end
+    end
+  end
+end
+
+#--gc0p4Jq0M2Yt08jU534c0p
+#Content-Type: application/x-Mascot; name="index"
+
+#parameters=4
+#masses=78
+#unimod=119
+#enzyme=484
+#header=492
+#summary=507
+#peptides=820
+#proteins=853
+#query1=858
+#query2=871
+#--gc0p4Jq0M2Yt08jU534c0p--

data/lib/mspire/mascot/dat/peptide.rb

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+
+module Mspire
+  module Mascot
+    class Dat
+      # mr = relative molecular mass; data contains keys of relative
+      Peptide = Struct.new(:missed_cleavages, :mr, :delta, :num_ions_matched, :seq, :peaks_from_ions_1, :var_mods_string, :ions_score, :ion_series_found, :peaks_from_ions_2, :peaks_from_ions_3, :query_num, :peptide_num, :proteins, :data) do
+        CAST = [:int, :float, :float, :int, :string, :int, :string, :float, :string, :int, :int]
+
+        # h49_q2 => [49, 2]; q2_p4_primary_nl => [2, 4, 'primary_nl] 
+        def self.qnum_pnum(string)
+          (qns, pns, other) = string.split('_', 3)
+          [ *[qns, pns].map {|ns| ns[1..-1].to_i }, other ]
+        end
+        # takes an io object (positioned at the beginning of a peptide hit)
+        # and reads off the next peptide hit "q1_p1=0,798.23...". Returns nil
+        # if it reaches the end of the section or it is a blank line
+        def self.from_io(io, proteins=false, data=false)
+          finished = ->(line) { line.size < 2 || line[0,2] == '--' }
+          line = io.readline("\n")
+          if finished[line]
+            nil
+          else
+            (qp, core, protein_info) = line.split(/[=;]/)
+            (qnum, pnum, _) = qnum_pnum(qp)
+            vals = core.split(',').zip(CAST).map do |val, cast| 
+              case cast
+              when :int then val.to_i
+              when :float then val.to_f
+              else 
+                val
+              end
+            end
+            pephit = self.new(*vals, qnum, pnum)
+            raise NotImplementedError, "not reading proteins or data yet" if proteins || data
+            loop do
+              before = io.pos
+              line = io.readline("\n")
+              if finished[line]
+                io.pos = before
+                break
+              end
+              (qp, string) = line.split('=')
+              (qnum, pnum, other) = qnum_pnum(qp)
+              if pephit.peptide_num != pnum || pephit.query_num != qnum
+                io.pos = before
+                break
+              end
+            end
+            pephit
+          end
+        end
+      end
+    end
+  end
+end
+
+=begin
+q1_p1=missed cleavages, (–1 indicates no match)
+    peptide Mr,
+    delta,
+    number of ions matched,
+    peptide string,
+    peaks used from Ions1,
+    variable modifications string,
+    ions score,
+    ion series found,
+    peaks used from Ions2,
+    peaks used from Ions3;
+    “accession string”: data for first protein
+        frame number:
+        start:
+        end:
+        multiplicity,
+    “accession string”: data for second protein
+        frame number:
+        start:
+        end:
+        multiplicity,
+    etc.
+q1_p1_et_mods=modification mass,
+    neutral loss mass,
+    modification description
+q1_p1_et_mods_master=neutral loss mass[[,neutral loss mass] ... ]
+q1_p1_et_mods_slave=neutral loss mass[[,neutral loss mass] ... ]
+q1_p1_primary_nl=neutral loss string
+q1_p1_na_diff=original NA sequence,
+    modified NA sequence
+q1_p1_tag=tagNum:startPos:endPos:seriesID,...
+q1_p1_drange=startPos:endPos
+q1_p1_terms=residue,residue[[:residue,residue] ... ]
+q1_p1_subst=pos1,ambig1,matched1 ... ,posn,ambign,matchedn
+q1_p1_comp=quantitation component name
+q1_p2=...
+=end
+

data/lib/mspire/mascot/dat/query.rb

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+require 'ostruct'
+require 'delegate'
+require 'cgi'
+
+module Mspire
+  module Mascot
+    class Dat
+      class Query < Hash
+
+        CAST = {
+          charge: ->(st) { (st[-1] << st[0...-1]).to_i },
+          title: ->(st) { CGI.unescape(st) },
+          mass_min: :to_f,
+          mass_max: :to_f,
+          int_min: :to_f,
+          int_max: :to_f,
+          num_vals: :to_i,
+          num_used1: :to_i,
+          index: :to_i,
+          Ions1: ->(st) { st.split(',').map {|pair_s| pair_s.split(':').map(&:to_f) } },
+        }
+
+        # returns self
+        def self.from_io(io)
+          query = self.new
+          while line = io.gets
+            break if line[0,2] == '--'
+            line.chomp!
+            (key, val) = line.split('=')
+            query[key.to_sym] = val
+          end
+          query.each do |k,v|
+            if cast=CAST[k]
+              apply = cast.is_a?(Symbol) ? cast.to_proc : cast
+              query[k] = apply[v] if apply
+            end
+          end
+          query
+        end
+
+        def method_missing(*args, &block)
+          if args[0].to_s[-1] == '='
+            if self.key?(args[0...-1])
+              self[ args[0...-1] ] = args[1]
+            else
+              super(*args, &block)
+            end
+          else
+            if self.key?(args[0])
+              self[ args[0] ]
+            else
+              super(*args, &block)
+            end
+          end
+        end
+      end
+    end
+  end
+end
+
+#index=1
+#charge=2+
+#mass_min=305.484440
+#mass_max=1998.945430
+#int_min=1.5
+#int_max=747
+#num_vals=3
+#num_used1=-1
+

data/lib/mspire/mascot/dat.rb

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+require 'mspire/mascot/dat/index'
+require 'mspire/mascot/dat/peptide'
+require 'mspire/mascot/dat/query'
+
+module Mspire
+  module Mascot
+    class Dat
+      # the io object which is the open dat file
+      attr_accessor :io
+
+      # the index object which points to the start byte for each section
+      attr_accessor :index
+
+      def initialize(io)
+        @io = io
+        @index = Index.new(@io)
+      end
+
+      def self.open(file, &block)
+        io = File.open(file)
+        block.call(self.new(io))
+        io.close
+      end
+
+      # positions io at the beginning of the section data (past the Content
+      # type and blank line). If given an integer, interprets it as a query
+      # number. returns self
+      def start_section!(name)
+        @io.pos = @index[name]
+        self
+      end
+
+      def query(n)
+        start_section!(n)
+        Query.from_io(@io)
+      end
+
+      def each_peptide(non_decoy=true, top_n=Float::INFINITY, &block)
+        block or return enum_for(__method__, non_decoy, top_n)
+        start_section!(non_decoy ? :peptides : :decoy_peptides)
+        while peptide = Peptide.from_io(@io)
+          block.call(peptide) if peptide.peptide_num <= top_n
+        end
+      end
+
+      # returns a list of all sections as symbols. The symbol :queries is
+      # returned rather than each query individually if their is 1 or more
+      # queries.
+      def sections
+        reply = @index.byte_num.keys
+        if @index.has_queries?
+          reply.push('queries')
+        end
+        reply.map(&:to_sym)
+      end
+
+    end
+  end
+end

data/mspire-mascot-dat.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "mspire-mascot-dat"
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["John T. Prince"]
+  s.date = "2013-03-28"
+  s.description = "Reads mascot dat files with gusto for mspire library."
+  s.email = "jtprince@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.md"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "LICENSE.txt",
+    "README.md",
+    "Rakefile",
+    "VERSION",
+    "lib/mspire/mascot/dat.rb",
+    "lib/mspire/mascot/dat/index.rb",
+    "lib/mspire/mascot/dat/peptide.rb",
+    "lib/mspire/mascot/dat/query.rb",
+    "mspire-mascot-dat.gemspec",
+    "spec/mspire/mascot/dat/index_spec.rb",
+    "spec/mspire/mascot/dat/peptide_spec.rb",
+    "spec/mspire/mascot/dat/query_spec.rb",
+    "spec/mspire/mascot/dat_spec.rb",
+    "spec/reference/dat_format_reference.md",
+    "spec/reference/two_spectra_decoy_F004129.png",
+    "spec/reference/two_spectra_no_decoy_F004128.png",
+    "spec/spec_helper.rb",
+    "spec/testfiles/F004128.dat",
+    "spec/testfiles/F004129.dat",
+    "spec/testfiles/two_spectra.mgf"
+  ]
+  s.homepage = "http://github.com/princelab/mspire-mascot-dat"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.23"
+  s.summary = "Reads mascot dat files for mspire library."
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<elif>, ["~> 0.1.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.8.0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
+    else
+      s.add_dependency(%q<elif>, ["~> 0.1.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.8.0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+    end
+  else
+    s.add_dependency(%q<elif>, ["~> 0.1.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.8.0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+  end
+end
+

data/spec/mspire/mascot/dat/index_spec.rb

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+require 'spec_helper'
+
+require 'mspire/mascot/dat/index'
+
+describe 'Mspire::Mascot::Dat::Index being initialized from file' do
+
+  let(:io) { File.open(TESTFILES + "/F004128.dat") }
+
+  specify '#initialize(io) creates the index object' do
+    Mspire::Mascot::Dat::Index.new(io).should be_a(Mspire::Mascot::Dat::Index)
+  end
+
+  describe Mspire::Mascot::Dat::Index do
+    subject { Mspire::Mascot::Dat::Index.new(io) }
+
+    it 'can access the header start byte nums' do
+
+      {
+        :parameters => 196,
+        :masses => 1203,
+        :unimod => 1873,
+        :enzyme => 20540,
+        :header => 20661,
+        :summary => 21103,
+        :peptides => 41624,
+        :proteins => 43894,
+      }.each {|head,val| subject[head].should == val }
+
+    end
+
+    it 'can get the queries' do
+      [1,2].zip([44129, 51186]) do |num, line_num|
+        subject.query(num).should == line_num
+      end
+    end
+
+    it 'can be accessed with brackets like array or hash' do
+      subject[1].should == 44129
+      subject[:peptides].should == 41624
+      subject['peptides'].should == 41624
+    end
+
+  end
+end

data/spec/mspire/mascot/dat/peptide_spec.rb

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+require 'spec_helper'
+
+require 'mspire/mascot/dat/peptide'
+
+describe 'reading off a Peptide' do
+
+  before(:all) do
+    info = <<STRING
+q2_p1=0,2978.269196,1.195840,5,MDSSSGSQGNGSFMDQNSLGILNMDNLK,17,000000000000001000000000100000,4.11,0002000020000000000,0,0;"Q9VV79":0:1:28:1
+q2_p1_terms=-,V
+q2_p1_primary_nl=000000000000002000000000200000
+q2_p2=1,2979.449478,0.015558,5,STGAESSEEXLREAYIMASVEHVNLLK,45,00000000000000000100000000000,2.84,0000000020000000000,0,0;"Q6SAG3":0:875:901:1 
+STRING
+    @io = StringIO.new(info)
+  end
+
+  it 'works' do
+    peptide = Mspire::Mascot::Dat::Peptide.from_io(@io)
+    { missed_cleavages: 0, mr: 2978.269196, delta: 1.19584, num_ions_matched: 5, seq: 'MDSSSGSQGNGSFMDQNSLGILNMDNLK', peaks_from_ions_1: 17, var_mods_string: '000000000000001000000000100000', ions_score: 4.11, ion_series_found: '0002000020000000000', peaks_from_ions_2: 0, peaks_from_ions_3: 0, query_num: 2, peptide_num: 1, proteins: nil, data: nil }.each do |k,v|
+      peptide.send(k).should == v
+    end
+  end
+
+end

data/spec/mspire/mascot/dat/query_spec.rb

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+require 'spec_helper'
+
+require 'mspire/mascot/dat/query'
+
+describe 'creating a query object' do
+
+  before(:all) do
+    # this is hacked up to be much smaller, so don't look for consistency
+    # between the data and the spectrum
+    data = <<END
+title=1%2e2746%2e2746%2e2
+index=1
+charge=2-
+mass_min=305.484440
+mass_max=1998.945430
+int_min=1.5
+int_max=747
+num_vals=3
+num_used1=-1
+Ions1=371.460240:10.3,486.498990:15.7,538.381160:24.9
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="query2"
+END
+    @io = StringIO.new(data)
+  end
+
+  it 'parses' do
+    query = Mspire::Mascot::Dat::Query.from_io(@io)
+    query.title.should == '1.2746.2746.2'
+    query.charge.should == -2
+  end
+end
+