ms-msrun 0.1.0 → 0.2.0

data/spec/ms/msrun_bm.rb

@@ -0,0 +1,22 @@
+require "ms/msrun"
+
+#Ms::Msrun.open("LPT_GFP_NUCLf.mzXML") do |ms| 
+Ms::Msrun.open("000.mzXML") do |ms| 
+  #indices = (1..1000).to_a
+  #start = Time.now
+  #indices.each do |n|
+  #  ms.scan(n).spectrum[0]
+  #end
+
+  start = Time.now
+  cnt = 0
+  ms.each do |scan|
+    scan.spectrum
+    cnt += 1
+  end
+
+  #puts "#{(Time.now - start) / indices.size} / scan"
+  #puts "#{Time.now - start} total secs for #{indices.size} scans"
+  puts "#{(Time.now - start) / cnt} / scan"
+  puts "#{Time.now - start} total secs for #{cnt} scans"
+end

data/spec/ms/msrun_spec.rb

@@ -3,156 +3,137 @@ require File.expand_path(File.dirname(__FILE__) + '/../spec_helper.rb')
 require 'ms/msrun'
 
 module MsrunSpec
-  extend Shareable
 
-  before do
-    @file = nil  # you need to define this!
-    @key = nil   # <- do nothing with this.
-    @nums = (1..20).to_a  # define scan numbers
+  before_all = lambda do |file|
+    nums = (1..20).to_a  # define scan numbers
+    key = YAML.load_file(file + '.key.yml')
+    [key, nums]
   end
 
-  def key
-    @key || @key = YAML.load_file(@file + '.key.yml')
-  end
+  shared 'an msrun object' do
 
-  def hash_match(hash, obj)
-    #$DEBUG = 1
-    puts "SCAN: #{obj.num}" if $DEBUG && obj.respond_to?(:num)
-    hash.each do |k,v|
-      if v.is_a?(Hash)
-        hash_match(v, obj.send(k.to_sym))
-      else
-        puts "#{k}: #{v} but was #{obj.send(k.to_sym)}" if obj.send(k.to_sym) != v
-        obj.send(k.to_sym).must_equal v
+    it 'reads header information' do
+      Ms::Msrun.open(@file) do |ms|
+        @key['header'].each do |k,v|
+          #puts "K: #{k} Vexp: #{v} Vact: #{ms.send(k.to_sym)}"
+          ms.send(k.to_sym).is v
+        end
       end
     end
-  end
 
-  it 'reads header information' do
-    Ms::Msrun.open(@file) do |ms|
-      key['header'].each do |k,v|
-        #puts "K: #{k} Vexp: #{v} Vact: #{ms.send(k.to_sym)}"
-        ms.send(k.to_sym).must_equal v
+    it 'can access random scans' do
+      Ms::Msrun.open(@file) do |ms|
+        scan = ms.scan(20)
+        hash_match(@key['scans'][20], scan)
       end
     end
-  end
 
-  it 'can access random scans' do
-    Ms::Msrun.open(@file) do |ms|
-      scan = ms.scan(20)
-      hash_match(key['scans'][20], scan)
-    end
-  end
-
-  it 'can read all scans' do
-    num_required_scans = key['scans'].size
-    Ms::Msrun.open(@file) do |ms|
-      ms.each do |scan|
-        if hash = key['scans'][scan.num]
-          hash_match(hash, scan)
-          num_required_scans -= 1
+    it 'can read all scans' do
+      num_required_scans = @key['scans'].size
+      Ms::Msrun.open(@file) do |ms|
+        ms.each do |scan|
+          if hash = @key['scans'][scan.num]
+            hash_match(hash, scan)
+            num_required_scans -= 1
+          end
         end
       end
+      num_required_scans.is 0
     end
-    num_required_scans.must_equal 0
-  end
 
-  it 'can read scans of a certain ms_level' do
-    nums = [1,5,9,13,17]
-    Ms::Msrun.open(@file) do |ms|
-      ms.each(:ms_level => 1) do |scan|
-        scan.num.must_equal nums.shift 
+    it 'can read scans of a certain ms_level' do
+      nums = [1,5,9,13,17]
+      Ms::Msrun.open(@file) do |ms|
+        ms.each(:ms_level => 1) do |scan|
+          scan.num.is nums.shift 
+        end
+      end
+      nums = [2,3,4,6,7,8,10,11,12,14,15,16,18,19,20]
+      Ms::Msrun.foreach(@file, :ms_level => 2) do |scan|
+        scan.num.is nums.shift 
       end
     end
-    nums = [2,3,4,6,7,8,10,11,12,14,15,16,18,19,20]
-    Ms::Msrun.foreach(@file, :ms_level => 2) do |scan|
-      scan.num.must_equal nums.shift 
-    end
-  end
 
-  it 'can avoid reading spectra' do 
-    nums = @nums.map
-    Ms::Msrun.foreach(@file, :spectrum => false) do |scan|
-      assert scan.spectrum.nil?
-      scan.num.must_equal nums.shift
+    it 'can avoid reading spectra' do 
+      nums = @nums.map
+      Ms::Msrun.foreach(@file, :spectrum => false) do |scan|
+        scan.spectrum.nil?.ok
+        scan.num.is nums.shift
+      end
     end
-  end
 
-  it 'can avoid reading precursor information' do 
-    Ms::Msrun.foreach(@file, :precursor => false) do |scan|
-      assert scan.precursor.nil?
+    it 'can avoid reading precursor information' do 
+      Ms::Msrun.foreach(@file, :precursor => false) do |scan|
+        scan.precursor.nil?.ok
+      end
     end
-  end
 
-  it 'gives scan counts for different ms levels' do
-    Ms::Msrun.open(@file) do |ms|
-      key['scan_count'].each do |index, count|
-        ms.scan_count(index).must_equal count
+    it 'gives scan counts for different ms levels' do
+      Ms::Msrun.open(@file) do |ms|
+        @key['scan_count'].each do |index, count|
+          ms.scan_count(index).is count
+        end
       end
     end
-  end
 
-  it 'gives start and end mz even if the information is not given' do
-    Ms::Msrun.open(@file) do |ms|
-      ms.start_and_end_mz_brute_force.must_equal(key['start_and_end_mz'][1])
+    it 'gives start and end mz even if the information is not given' do
+      Ms::Msrun.open(@file) do |ms|
+        ms.start_and_end_mz_brute_force.is(@key['start_and_end_mz'][1])
+      end
     end
   end
 
-end
-
-class Mzxml_v1 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
+  describe 'reading an mzXML v1 file' do
     @file = TESTFILES + '/opd1/000.v1.mzXML'
-  end
+    
+    (@key, @nums) = before_all.call(@file)
+
 
-  it 'can give start and end mz' do
-    # scan has attributes startMz endMz
-    Ms::Msrun.open(@file) do |ms|
-      #ms.start_and_end_mz.must_equal([300.0, 1500.0])
-      ms.start_and_end_mz.must_equal(key['start_and_end_mz'][1])
+    it 'can give start and end mz' do
+      # scan has attributes startMz endMz
+      Ms::Msrun.open(@file) do |ms|
+        #ms.start_and_end_mz.is([300.0, 1500.0])
+        ms.start_and_end_mz.is @key['start_and_end_mz'][1]
+      end
     end
+
+    behaves_like 'an msrun object'
+
   end
-end
 
-class Mzxml_v2_0 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
+  describe 'reading an mzXML v2.0 file' do
     @file = TESTFILES + '/opd1/020.v2.0.readw.mzXML'
+    (@key, @nums) = before_all.call(@file)
+    behaves_like 'an msrun object'
   end
-end
 
-class Mzxml_v2_1 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
+  describe 'reading an mzXML v2.1 file' do
     @file = TESTFILES + '/opd1/000.v2.1.mzXML'
-  end
+    (@key, @nums) = before_all.call(@file)
+    behaves_like 'an msrun object'
 
-  it 'gives nil if scans do not have start and end mz info' do
-    # scans do not have startMz endMz or filterLine
-    Ms::Msrun.open(@file) do |ms|
-      ms.start_and_end_mz.must_equal([nil, nil])
+    it 'gives nil if scans do not have start and end mz info' do
+      # scans do not have startMz endMz or filterLine
+      Ms::Msrun.open(@file) do |ms|
+        ms.start_and_end_mz.is([nil, nil])
+      end
     end
-  end
 
-  it 'gives start and end mz if filterLine present' do
-    newname = @file + ".TMP.mzXML"
-    File.open(newname, 'w') do |out|
-      IO.foreach(@file) do |line|
-        if line =~ /msLevel="1"/
-          out.puts %Q{        filterLine="FTMS + p NSI Full ms [300.00-1500.00]"}
+    it 'gives start and end mz if filterLine present' do
+      newname = @file + ".TMP.mzXML"
+      File.open(newname, 'w') do |out|
+        IO.foreach(@file) do |line|
+          if line =~ /msLevel="1"/
+            out.puts %Q{        filterLine="FTMS + p NSI Full ms [300.00-1500.00]"}
+          end
+          out.print line
         end
-        out.print line
       end
+      Ms::Msrun.open(newname) do |ms|
+        ms.start_and_end_mz.is([300.0, 1500.0])
+      end
+      File.unlink(newname) if File.exist?(newname)
     end
-    Ms::Msrun.open(newname) do |ms|
-      ms.start_and_end_mz.must_equal([300.0, 1500.0])
-    end
-    File.unlink(newname) if File.exist?(newname)
-  end
 
+  end
 end
-

data/spec/ms/scan_spec.rb

@@ -2,7 +2,7 @@ require File.expand_path(File.dirname(__FILE__) + '/../spec_helper')
 
 require 'ms/msrun'
 
-class ScanUnitSpec < MiniTest::Spec
+describe 'a scan' do
 
   before do
     @scan = Ms::Scan.new
@@ -10,25 +10,24 @@ class ScanUnitSpec < MiniTest::Spec
     @scan.spectrum = Ms::Spectrum.new([[1,2,3,4], [2,4,4,2]])
   end
 
-
- it 'determines if its +1 or not' do
+ it 'can determine if its +1 or not' do
     # these have not been checked for accuracy, just sanity
     reply = [0.1,2.5, 3.5, 5].map do |prec_mz|
       @scan.precursor.mz = prec_mz
       @scan.plus1?(-0.1)
     end
-    reply.all? {|v| v == true }.must_equal true
+    reply.all? {|v| v == true }.ok
 
     reply = [0.1,2.5, 3.5, 5].map do |prec_mz|
       @scan.precursor.mz = prec_mz
       @scan.plus1?(1.0)
     end
-    reply.all? {|v| v == false }.must_equal true
+    reply.all? {|v| v == false }.ok
 
     reply = [0.1,2.5, 3.5, 5].map do |prec_mz|
       @scan.precursor.mz = prec_mz
       @scan.plus1?(0.5)
     end
-    reply.must_equal [false, false, true, true]
+    reply.enums [false, false, true, true]
   end
 end

data/spec/ms/spectrum/compare_spec.rb

@@ -9,42 +9,45 @@ class Array
   end
 end
 
-class CompareSpec < MiniTest::Spec
+module CompareSpec
   include Ms
 
-  before do
-    @a = Spectrum.new([[0,2,3,4], [5,6,7,8]])
-    @b = Spectrum.new([[0, 1.5, 3.5, 5.5], [9,10,11,12]])
+  describe 'comparison of spectra' do
 
-    @c = Spectrum.new([[0, 1], [8,9]])
-    @d = Spectrum.new([[0.6, 0.75], [10,11]])
-  end
+    before do
+      @a = Spectrum.new([[0,2,3,4], [5,6,7,8]])
+      @b = Spectrum.new([[0, 1.5, 3.5, 5.5], [9,10,11,12]])
 
-  it 'compares spectra' do
-    # array form:
-    @c.compare(@d).rev_ab.must_equal( @d.compare(@c) )
-    @c.compare(@d).must_equal [[8, 10, 0.6]]
+      @c = Spectrum.new([[0, 1], [8,9]])
+      @d = Spectrum.new([[0.6, 0.75], [10,11]])
+    end
 
-    # block form
-    exp = [[5,9], [6,10], [7,11]]
-    # default radius 1.0
-    @a.compare(@b) do |int_a, int_b| 
-     exp.delete([int_a, int_b])
+    it 'compares spectra' do
+      # array form:
+      @c.compare(@d).rev_ab.is( @d.compare(@c) )
+      @c.compare(@d).is [[8, 10, 0.6]]
+
+      # block form
+      exp = [[5,9], [6,10], [7,11]]
+      # default radius 1.0
+      @a.compare(@b) do |int_a, int_b| 
+        exp.delete([int_a, int_b])
+      end
+      exp.size.is 0
     end
-    exp.size.must_equal 0
-  end
 
-  it 'computes similarity score' do
-    @a.sim_score(@a, :radius => 0.1).must_equal 1.0
-    # this is just frozen, not verified:
-    @a.sim_score(@b).must_be_close_to 0.702945603476432, 0.000001
-  end
+    it 'computes similarity score' do
+      @a.sim_score(@a, :radius => 0.1).is 1.0
+      # this is just frozen, not verified:
+      @a.sim_score(@b).should.be.close 0.702945603476432, 0.000001
+    end
 
-  it 'computes a pic score' do
-    @a.pic_score(@a, :radius => 0.01).must_equal 100.0
-    @a.pic_score(@d, :radius => 0.01).must_equal 0.0
-    # frozen:
-    @a.pic_score(@b).must_be_close_to 68.4981684981685, 0.000001 
+    it 'computes a pic score' do
+      @a.pic_score(@a, :radius => 0.01).is 100.0
+      @a.pic_score(@d, :radius => 0.01).is 0.0
+      # frozen:
+      @a.pic_score(@b).should.be.close 68.4981684981685, 0.000001 
+    end
   end
 end
 

data/spec/ms/spectrum/filter_spec.rb

@@ -10,24 +10,26 @@ class Array
   end
 end
 
-class FilterSpec < MiniTest::Spec
+class FilterSpec
   include Ms
 
-  before do
-    @a = Spectrum.new([[0,5,10, 15,16,17,18, 20.1], [0,1,2, 3,8,10,4, 0]])
-    @null = Spectrum.new([[],[]])
-  end
+  describe 'filtering spectra' do
+    before do
+      @a = Spectrum.new([[0,5,10, 15,16,17,18, 20.1], [0,1,2, 3,8,10,4, 0]])
+      @null = Spectrum.new([[],[]])
+    end
 
-  it 'filters spectra' do
-    spec = @a.filter(:bins, :bin_width => 10, :num_peaks => 2)
-    spec.mzs.must_equal [5,10,16,17,20.1]
-    spec.intensities.must_equal [1,2,8,10,0]
+    it 'filters spectra' do
+      spec = @a.filter(:bins, :bin_width => 10, :num_peaks => 2)
+      spec.mzs.enums [5,10,16,17,20.1]
+      spec.intensities.enums [1,2,8,10,0]
 
-    @a.filter(:bins, :bin_width => 100, :num_peaks => 8).must_equal @a
-    @a.filter(:bins, :bin_width => 1, :num_peaks => 1).must_equal @a
-    @a.filter(:bins, :bin_width => 1, :num_peaks => 0).must_equal @null
-  end
+      @a.filter(:bins, :bin_width => 100, :num_peaks => 8).is @a
+      @a.filter(:bins, :bin_width => 1, :num_peaks => 1).is @a
+      @a.filter(:bins, :bin_width => 1, :num_peaks => 0).is @null
+    end
 
+  end
 end
 
 

data/spec/spec_helper.rb

@@ -0,0 +1,21 @@
+require 'rubygems'
+require 'spec/more'
+
+TESTFILES = File.expand_path(File.dirname(__FILE__)) + '/testfiles'
+
+module Bacon
+  class Context
+    def hash_match(hash, obj)
+      hash.each do |k,v|
+        if v.is_a?(Hash)
+          hash_match(v, obj.send(k.to_sym))
+        else
+          puts "#{k}: #{v} but was #{obj.send(k.to_sym)}" if obj.send(k.to_sym) != v
+          obj.send(k.to_sym).should.equal v
+        end
+      end
+    end
+  end
+end
+
+Bacon.summary_on_exit