mascot-mgf 0.2.0

data/.gitignore

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+pkg/*
+*.gem
+.bundle
+*.idx

data/Gemfile

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+source "http://rubygems.org"
+
+# Specify your gem's dependencies in mascot-mgf.gemspec
+gemspec

data/README.rdoc

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+= Mascot::MGF
+
+A parser for Mascot Generic Format (MGF) files.
+
+== MGF Format 
+
+The Mascot::MGF object represents a file of MSMS spectra. See http://www.matrixscience.com/help/data_file_help.html#GEN for more
+information on this file format.
+
+
+== Mascot::MGF
+
+A subclass of File, opens an MGF flat file to read entries using Enumerable syntax.
+
+== Mascot::MGF::Query
+
+A simple object that represents individual MS/MS spectrum objects in an MGF file. I use "Query" instead of "Spectrum" to remain consistent with Mascot''s terminology.
+
+== Simple Usage Examples
+
+=== Reading 
+
+    require 'mascot/mgf'
+
+    # This opens a MGF file and builds an index of the query 
+    # positions. The index is cached to the filesystem.
+    mgf = Mascot::MGF.open("some/file/path.mgf")
+
+    # Same thing as above, but does not cache the index to filesystem
+    mgf = Mascot::MGF.open("some/file/path.mgf",false)
+
+    # How many queries are in this file?
+    mgf.query_count
+		# Reads the next query from the read cursor position
+    query_string = mgf.readquery()
+
+		# Create a Mascot::MGF::Query from the query string
+		query = Mascot::Query.new(query_string)
+    puts query.title
+
+		# Read the next query as a Mascot::MGF::Query object
+		query = mgf.query()
+		puts query.title
+
+		# puts cursor at begining of MGF file
+		mgf.rewind
+    mgf.each_query do |query_object|
+      # do something with query...
+    end
+		
+

data/Rakefile

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+require 'bundler'
+Bundler::GemHelper.install_tasks
+
+require 'rake/testtask'
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/test*.rb']
+  t.verbose = true
+end

data/lib/mascot/mgf.rb

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+module Mascot
+  class MGF < File
+    require 'mascot/mgf/query'
+    attr_reader :idx, :full_path, :curr_index
+    def initialize(mgf_file_path,cache_index=true,open_mode="r")
+      super(mgf_file_path, open_mode)
+      @full_path = File.expand_path(mgf_file_path)
+      @cache_index = cache_index
+      @curr_index = 0
+      @idx = {}
+      parse_index()
+    end
+
+    def rewind
+      super
+      @curr_index = 0      
+    end
+    
+    def readquery(n=nil)
+      if n
+        @curr_index = n
+      end
+      self.pos = @idx[@curr_index][0]
+      bytelength = @idx[@curr_index][1] - @idx[@curr_index][0]
+      @curr_index += 1
+      self.read(bytelength)
+    end
+    
+    def each_query
+      while !self.eof?
+        yield self.query() if block_given?
+      end
+    end
+
+    # alias_method :io_each, :each 
+    # def each 
+    #   while !self.eof?
+    #     yield self.readquery if block_given?
+    #   end
+    # end
+
+    def query(n=nil)
+      Mascot::MGF::Query.new(self.readquery(n))
+    end
+    
+    # reports how many queries are in this MGF file
+    def query_count()
+      return @idx.length
+    end
+
+    private
+
+    def parse_index()
+      if File.exists?(@full_path + ".idx")
+        # read the index from file
+        idx_file = File.open(@full_path + ".idx",'rb')
+        @idx = ::Marshal.load(idx_file)
+        idx_file.close
+      else
+        create_index()
+      end
+    end
+
+    def create_index()
+      @idx = []
+      # state tracker, 0 => not in a ions boundary, 1 => in a query
+      ion_boundary_state = 0
+      self.rewind
+      self.grep(/^(\w+) IONS$/) do |l|
+        case $1
+        when "BEGIN"
+          @idx << [self.pos - l.length, nil]
+        when "END"
+          @idx[-1][1] = self.pos
+        end
+      end   
+      if @cache_index
+        idx_file = File.open(@full_path + ".idx",'wb')
+        idx_file.print(::Marshal.dump(@idx))
+        idx_file.close
+      end
+      # place cursor at beginning of file again
+      self.rewind
+    end
+  end
+end

data/lib/mascot/mgf/query.rb

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+module Mascot
+  class MGF
+    class Query
+
+      attr_accessor :ions, :title, :pepmass, :entry, :charge
+
+      # Initializes a spectrum entry from a MGF formatted string or from an Array
+      # that is the newline split of MGF 'BEGIN IONS\n...\nEND IONS'
+      def initialize(entry=nil)
+        if entry.kind_of? String
+          entry = entry.split(/\n/)
+        end
+        @title = 'id=1'
+        @pepmass = []
+        @atts = {}
+        @ions = []
+        @charge = nil
+        parse(entry)
+      end
+
+      # Returns the formatted MGF entry string
+      def to_s
+        tmp = "BEGIN IONS\nTITLE=#{@title}\n"
+        tmp += "PEPMASS=#{@pepmass.join(' ')}\n" if @pepmass.length > 0
+        tmp += "CHARGE=#{@charge}+\n" if @charge
+        @atts.each_pair do |k,v|
+          tmp += "#{k.to_s.upcase}=#{v}\n"
+        end
+        tmp += @ions.collect { |i| i.join(" ")}.join("\n")
+        tmp += "\nqEND IONS\n"
+        return tmp
+      end
+
+      def method_missing(m)
+        if @atts.has_key? m.to_sym
+          return @atts[m.to_sym]
+        else
+          return nil
+        end
+      end
+
+      private
+
+      def parse(entry)
+        return nil if entry.nil?
+        entry.each do |ln|
+          if ln =~ /(\w+)=(.+)/
+            case $1
+            when "PEPMASS"
+              @pepmass = $2.split(/\s/).collect {|e| e.to_f }
+            when "TITLE"
+              @title = $2
+            when "CHARGE"
+              @charge = $2.to_i
+            else
+              @atts[$1.downcase.to_sym] = $2
+            end
+          elsif ln =~ /^\d+/
+            tmp = ln.split(/\s+/).map {|e| e.to_f }
+            @ions << tmp
+          else
+            next
+          end
+        end
+      end
+    end
+  end
+end

data/lib/mascot/mgf/version.rb

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+module Mascot
+  class MGF
+    VERSION = "0.2.0"
+  end
+end

data/mascot-mgf.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "mascot/mgf/version"
+
+Gem::Specification.new do |s|
+  s.name        = "mascot-mgf"
+  s.version     = Mascot::MGF::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Angel Pizarro"]
+  s.email       = ["delagoya@gmail.com"]
+  s.homepage    = "https://github.com/delagoya/mascot-mgf"
+  s.summary     = %q{A parser for Mascot Generic Format (MGF) files}
+  s.description = s.summary
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+end

data/test/fixtures/example.mgf

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data/test/fixtures/first_query.mgf

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+BEGIN IONS
+TITLE=example.9.9.2
+RTINSECONDS=318.0218
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+CHARGE=2
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+END IONS

data/test/fixtures/second_query.mgf

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+BEGIN IONS
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+RTINSECONDS=319.7966
+PEPMASS=1018.52 563.95965576171875
+CHARGE=2
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+END IONS

data/test/fixtures/tenth_query.mgf

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+BEGIN IONS
+TITLE=example.123.123.2
+RTINSECONDS=760.3257
+PEPMASS=643.77874755859375 367.44775390625
+CHARGE=2
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+END IONS

data/test/fixtures/titles.yml

@@ -0,0 +1,14 @@
+--- 
+- example.9.9.2
+- example.10.10.2
+- example.11.11.3
+- example.12.12.2
+- example.13.13.3
+- example.85.85.2
+- example.117.117.2
+- example.118.118.2
+- example.119.119.3
+- example.123.123.2
+- example.124.124.3
+- example.160.160.2
+- example.165.165.2

data/test/test_mascot-mgf.rb

@@ -0,0 +1,82 @@
+require 'test/unit'
+require 'mascot/mgf'
+class TestMascotMgf < Test::Unit::TestCase
+  def setup
+    @mgf_file = File.open(File.expand_path("test/fixtures/example.mgf"))
+  end
+
+  def test_canary
+    assert true, "The canary does not sing"
+  end
+  
+  def test_open_file
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert_not_nil mgf
+  end
+  
+  def test_get_first_and_second_query_string
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert_not_nil mgf
+    first_query =File.read("test/fixtures/first_query.mgf")
+    # first_query = first_query.strip.chomp
+    assert_equal(first_query,mgf.readquery())
+    second_query =File.read("test/fixtures/second_query.mgf")
+    # second_query = second_query.strip.chomp
+    assert_equal( second_query,mgf.readquery())
+  end
+
+  def test_get_tenth_query_string
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert_not_nil mgf
+    tenth_query =File.read("test/fixtures/tenth_query.mgf")
+    # move cursor to tenth query
+    assert_equal(tenth_query,mgf.readquery(9))
+  end
+
+  def test_get_tenth_query_object
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert_not_nil mgf
+    # BEGIN IONS
+    # TITLE=example.123.123.2
+    # RTINSECONDS=760.3257
+    # PEPMASS=643.77874755859375 367.44775390625
+    # CHARGE=2
+    tenth_query_title = 'example.123.123.2'
+    tenth_query_rtinseconds = 760.3257
+    tenth_query_pepmass = [643.77874755859375, 367.44775390625]
+    tenth_query_charge = 2
+    # move cursor to tenth query
+    tenth_query = mgf.query(9)
+    assert_equal(tenth_query_title, tenth_query.title)
+    assert_equal(tenth_query_rtinseconds, tenth_query_rtinseconds)
+    assert_equal(tenth_query_charge, tenth_query.charge)
+    assert_equal(tenth_query_pepmass[0], tenth_query.pepmass[0])
+    assert_equal(tenth_query_pepmass[1], tenth_query.pepmass[1])
+  end
+  
+  def test_query_count
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert_equal(13, mgf.query_count)
+  end
+
+  def test_create_cached_index
+    mgf = Mascot::MGF.open(@mgf_file)
+    assert(File.exists?(mgf.full_path + ".idx"))
+  end
+  def test_skip_cached_index
+    # delete the index if it exists
+    File.unlink(@mgf_file.path + ".idx")
+    mgf = Mascot::MGF.open(@mgf_file,false)
+    assert(!File.exists?(mgf.full_path + ".idx"))
+  end
+  def test_rewind_override
+    mgf = Mascot::MGF.open(@mgf_file,false)
+    first_query = mgf.query()
+    second_query = mgf.query()
+    mgf.rewind
+    assert_equal(0,mgf.curr_index)
+    assert_equal(first_query.title, mgf.query().title)
+    assert_equal(1,mgf.curr_index)
+    assert_equal(second_query.title, mgf.query().title)
+  end
+end

metadata

@@ -0,0 +1,83 @@
+--- !ruby/object:Gem::Specification 
+name: mascot-mgf
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 2
+  - 0
+  version: 0.2.0
+platform: ruby
+authors: 
+- Angel Pizarro
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-01-10 00:00:00 -05:00
+default_executable: 
+dependencies: []
+
+description: A parser for Mascot Generic Format (MGF) files
+email: 
+- delagoya@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- .gitignore
+- Gemfile
+- README.rdoc
+- Rakefile
+- lib/mascot/mgf.rb
+- lib/mascot/mgf/query.rb
+- lib/mascot/mgf/version.rb
+- mascot-mgf.gemspec
+- test/fixtures/example.mgf
+- test/fixtures/first_query.mgf
+- test/fixtures/second_query.mgf
+- test/fixtures/tenth_query.mgf
+- test/fixtures/titles.yml
+- test/test_mascot-mgf.rb
+has_rdoc: true
+homepage: https://github.com/delagoya/mascot-mgf
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: A parser for Mascot Generic Format (MGF) files
+test_files: 
+- test/fixtures/example.mgf
+- test/fixtures/first_query.mgf
+- test/fixtures/second_query.mgf
+- test/fixtures/tenth_query.mgf
+- test/fixtures/titles.yml
+- test/test_mascot-mgf.rb