ms-sequest 0.0.16 → 0.0.17

data/Gemfile

@@ -0,0 +1,18 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "ms-core", ">= 0.0.11"
+gem "arrayclass", ">= 0.1.0"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "ms-testdata", ">= 0.1.1"
+  gem "spec-more", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+end
+
+

data/Gemfile.lock

@@ -0,0 +1,30 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    arrayclass (0.1.1)
+    bacon (1.1.0)
+    bio (1.4.1)
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    ms-core (0.0.11)
+      bio (>= 1.4.1)
+    ms-testdata (0.1.1)
+    rake (0.8.7)
+    rcov (0.9.9)
+    spec-more (0.0.4)
+      bacon
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  arrayclass (>= 0.1.0)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  ms-core (>= 0.0.11)
+  ms-testdata (>= 0.1.1)
+  rcov
+  spec-more

data/Rakefile

@@ -1,40 +1,36 @@
 require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
 require 'rake'
-require 'jeweler'
-require 'rake/testtask'
-require 'rcov/rcovtask'
-
-NAME = "ms-sequest"
-
-gemspec = Gem::Specification.new do |s|
-  s.name = NAME
-  s.authors = ["John T. Prince"]
-  s.email = "jtprince@gmail.com"
-  s.homepage = "http://github.com/jtprince/" + NAME
-  s.summary = "An mspire library supporting SEQUEST, Bioworks, SQT, etc"
-  s.description = "reads .SRF, .SQT and supports conversions"
-  s.rubyforge_project = 'mspire'
-
-  s.add_dependency("arrayclass", ">= 0.1.0")
-  s.add_dependency("ms-core", ">= 0.0.2")
-  s.add_dependency("ms-fasta", ">= 0.4.1")
 
-  s.add_development_dependency("ms-testdata", ">= 0.18.0")
-  s.add_development_dependency("spec-more")
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  gem.name = "ms-sequest"
+  gem.homepage = "http://github.com/jtprince/ms-sequest"
+  gem.license = "MIT"
+  gem.summary = %Q{An mspire library supporting SEQUEST, Bioworks, SQT, etc}
+  gem.description = %Q{reads .SRF, .SQT and supports conversions}
+  gem.email = "jtprince@gmail.com"
+  gem.authors = ["John T. Prince"]
+  gem.rubyforge_project = 'mspire'
+  # include dependencies in Gemfile
 end
-Jeweler::Tasks.new(gemspec)
-
-Rake::TestTask.new(:spec) do |t|
-  t.libs << 'lib' << 'spec'
-  t.pattern = 'spec/**/*_spec.rb'
-  t.verbose = true
-  unless ENV['gems']
-    t.libs << 'submodule/ms-testdata/lib'
-    #t.libs << 'submodule/ms-in_silico/lib'
-    #t.libs << 'submodule/tap-mechanize/lib'
-  end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
 end
 
+require 'rcov/rcovtask'
 Rcov::RcovTask.new do |spec|
   spec.libs << 'spec'
   spec.pattern = 'spec/**/*_spec.rb'
@@ -43,3 +39,22 @@ end
 
 task :default => :spec
 
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "ms-sequest #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+
+
+
+
+
+
+
+
+

data/VERSION

@@ -1 +1 @@
-0.0.16
+0.0.17

data/lib/ms/sequest/sqt.rb

@@ -70,8 +70,10 @@ module Ms
         total_sequence_length = 0
         fastasize = 0
         Ms::Fasta.open(dbfile) do |fasta|
-          fasta.each {|entry| total_sequence_length += entry.sequence.size }
-          fastasize = fasta.size
+          fasta.each do |entry| 
+            total_sequence_length += entry.sequence.size 
+            fastasize += 1
+          end
         end
         [total_sequence_length, fastasize]
       end

data/spec/ms/sequest/sqt_spec.rb

@@ -1,7 +1,6 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-
-require File.dirname(__FILE__) + '/sqt_spec_helper'
+require 'spec_helper'
 
+require 'ms/sequest/sqt_spec_helper'
 require 'ms/sequest/sqt'
 
 describe 'reading a small sqt file' do

data/spec/ms/sequest/srf/search_spec.rb

@@ -1,35 +1,84 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../../spec_helper' )
-require File.expand_path( File.dirname(__FILE__) + '/search_spec_helper' )
-
+require 'spec_helper'
 require 'fileutils'
 
 require 'ms/sequest/srf'
 require 'ms/sequest/srf/search'
 
+class SRF_TO_MGF_HELPER
+  FIRST_MSMS = {
+    :first_lines => ['BEGIN IONS', 'TITLE=000.2.2.1.dta', 'CHARGE=1+', 'PEPMASS=391.04541015625'],
+    :first_two_ion_lines => ['111.976043701172 41418.0', '112.733383178711 88292.0'],
+    :last_two_ion_lines => ['407.412780761719 18959.0', '781.085327148438 10104.0'],
+    :last_line => 'END IONS',
+  }
+  LAST_MSMS = { 
+    :first_lines => ['BEGIN IONS', 'TITLE=000.3748.3748.3.dta', 'CHARGE=3+', 'PEPMASS=433.56494098625'],
+    :first_two_ion_lines => ['143.466918945312 2110.0', '151.173095703125 4134.0'],
+    :last_two_ion_lines => ['482.678771972656 3357.0', '610.4111328125 8968.0'],
+    :last_line => 'END IONS',
+  }
+end
+
+# these have been checked against Bioworks .dta output
+class SRF_TO_DTA_HELPER
+  FIRST_SCAN = {
+    :first_line => '391.045410 1',
+    :first_two_ion_lines => ['111.9760 41418', '112.7334 88292'],
+    :last_two_ion_lines => ['407.4128 18959', '781.0853 10104'],
+  }
+  LAST_SCAN = {
+    :first_line => '1298.680271 3',
+    :first_two_ion_lines => ['143.4669 2110', '151.1731 4134'],
+    :last_two_ion_lines => ['482.6788 3357', '610.4111 8968'],
+  }
+end
+
 Srf_file = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf'
-Mgf_output = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.mgf.tmp'
-Dta_output = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.dta.tmp'
+TMPDIR = TESTFILES + '/tmp'
+Mgf_output = TMPDIR + '/000.mgf.tmp'
+Dta_output = TMPDIR + '/000.dta.tmp'
+
 shared 'an srf to ms2 search converter' do
+  def assert_ion_line_close(expected, actual, delta)
+    expected.split(/\s+/).zip(actual.split(/\s+/)).each do |exp,act|
+      exp.to_f.should.be.close act.to_f, delta
+    end
+  end
 
-  def del(file)
-    if File.exist?(file)
-      if File.directory?(file)
-        FileUtils.rm_rf(file)
-      else
-        File.unlink(file)
-      end
+  def compare_dtas(key, filename)
+    ok File.exist?(filename) 
+    lines = IO.read(filename).strip.split("\n")
+    (exp1, act1) = [key[:first_line], lines[0]].map {|l| l.split(/\s+/) }
+    exp1.first.to_f.should.be.close act1.first.to_f, 0.000001
+    exp1.last.is act1.last
+    (key[:first_two_ion_lines] + key[:last_two_ion_lines]).zip(lines[1,2]+lines[-2,2]) do |exp,act|
+      assert_ion_line_close(exp, act, 0.0001)
     end
   end
 
+  def compare_mgfs(key, string_chunk)
+    lines = string_chunk.strip.split("\n")
+    key[:first_lines][0,3].enums lines[0,3]
+    (exp_pair, act_pair) = [key[:first_lines][3], lines[3]].map {|line| line.split('=') }
+    exp_pair.first.is act_pair.first
+    exp_pair.last.to_f.should.be.close act_pair.last.to_f, 0.00000000001
+
+    (key[:first_two_ion_lines] + key[:last_two_ion_lines]).zip(lines[4,2] + lines[-3,2]).each do |exp_line,act_line|
+      assert_ion_line_close(exp_line, act_line, 0.00000001)
+    end
+
+    key[:last_line].is lines[-1]
+  end
+
   it 'converts to mgf' do
     @output = Mgf_output
     @convert_to_mgf.call
     ok File.exist?(@output)
     output = IO.read(@output)
-    # tests are just frozen right now, not checked for accuracy
-    ok output.include?(SRF_TO_MGF_HELPER::FIRST_MSMS)
-    ok output[1000..-1].include?(SRF_TO_MGF_HELPER::LAST_MSMS)
-    del(@output)
+    chunks = output.split("\n\n")
+
+    compare_mgfs(SRF_TO_MGF_HELPER::FIRST_MSMS, chunks.first)
+    compare_mgfs(SRF_TO_MGF_HELPER::LAST_MSMS, chunks.last)
   end
 
   it 'generates .dta files' do
@@ -40,19 +89,20 @@ shared 'an srf to ms2 search converter' do
     # frozen (not verified):
     Dir[@output + "/*.*"].size.is 3893 # the correct number files
 
-    first_file = @output + '/000.2.2.1.dta'
-    ok File.exist?(first_file) 
-    IO.read(first_file).is SRF_TO_DTA_HELPER::FIRST_SCAN.gsub("\n", "\r\n")
-    last_file = @output + '/000.3748.3748.3.dta'
-    IO.read(last_file).is SRF_TO_DTA_HELPER::LAST_SCAN.gsub("\n", "\r\n")
-
-    del(@output)
+    compare_dtas(SRF_TO_DTA_HELPER::FIRST_SCAN, @output + '/000.2.2.1.dta')
+    compare_dtas(SRF_TO_DTA_HELPER::LAST_SCAN, @output + '/000.3748.3748.3.dta')
   end
 
 end
 
-
 describe 'converting an srf to ms2 search format: programmatic' do
+  before do
+    FileUtils.mkdir(TMPDIR) unless File.exist?(TMPDIR)
+  end
+  after do
+    FileUtils.rmtree(TMPDIR)
+  end
+
   @srf = Ms::Sequest::Srf.new(Srf_file)
 
   @convert_to_mgf = lambda { @srf.to_mgf(Mgf_output) }
@@ -63,6 +113,12 @@ describe 'converting an srf to ms2 search format: programmatic' do
 end
 
 describe 'converting an srf to ms2 search format: commandline' do
+  before do
+    FileUtils.mkdir(TMPDIR) unless File.exist?(TMPDIR)
+  end
+  after do
+    FileUtils.rmtree(TMPDIR)
+  end
 
   def commandline_lambda(string)
     lambda { Ms::Sequest::Srf::Search.commandline(string.split(/\s+/)) }

data/spec/ms/sequest/srf/sqt_spec.rb

@@ -1,4 +1,4 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../../spec_helper' )
+require 'spec_helper'
 
 require 'ms/sequest/srf'
 require 'ms/sequest/srf/sqt'
@@ -25,6 +25,11 @@ ExpasyStaticMods = ['C=160.1901','Cterm=10.1230','E=161.4455']
 MoleculesStaticMods = ["C=160.1942", "Cterm=10.1230", "E=161.44398"]
 SpecHelperHeaderHash['StaticMod'] = MoleculesStaticMods 
 
+# these only need to be really close
+Close_indices = {
+  'S' => [6,7],
+  'M' => [3,4,5,6],
+}
 
 SpecHelperOtherLines =<<END
 S	2	2	1	0.0	VELA	391.04541015625	3021.5419921875	0.0	0
@@ -42,7 +47,8 @@ END
 
 module SPEC
   Srf_file = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf' 
-  Srf_output = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.sqt.tmp'
+  TMPDIR = TESTFILES + '/tmp'
+  Srf_output = TMPDIR + '/000.sqt.tmp'
 end
 
 shared 'an srf to sqt converter' do
@@ -88,6 +94,23 @@ shared 'an srf to sqt converter' do
     end
   end
 
+  def sqt_line_match(act_line_ar, exp_line_ar)
+    exp_line_ar.zip(act_line_ar) do |exp_line, act_line|
+      (e_pieces, a_pieces) = [exp_line, act_line].map {|line| line.chomp.split("\t") } 
+      if %w(S M).include?(k = e_pieces[0])
+        (e_close, a_close) = [e_pieces, a_pieces].map do |pieces| 
+          Close_indices[k].sort.reverse.map do |i|
+            pieces.delete_at(i).to_f
+          end.reverse
+        end
+        e_close.zip(a_close) do |ex, ac|
+          ex.should.be.close ac, 0.0000001
+        end
+      end
+      e_pieces.enums a_pieces
+    end
+  end
+
   it 'converts without bothering with the database' do
     @basic_conversion.call
     ok File.exist?(@output)
@@ -97,8 +120,10 @@ shared 'an srf to sqt converter' do
     ok(header_lines.size > 10)
     ok header_hash_match(header_lines, SpecHelperHeaderHash)
     other_lines = lines.grep(/^[^H]/)
-    other_lines[0,4].join('').is SpecHelperOtherLines
-    other_lines[-3,3].join('').is SpecHelperOtherLinesEnd
+
+    sqt_line_match(other_lines[0,4], SpecHelperOtherLines.strip.split("\n"))
+    sqt_line_match(other_lines[-3,3], SpecHelperOtherLinesEnd.strip.split("\n"))
+
     del(@output)
   end
 
@@ -134,6 +159,12 @@ shared 'an srf to sqt converter' do
 end
 
 describe "programmatic interface srf to sqt" do
+  before do
+    FileUtils.mkdir(SPEC::TMPDIR) unless File.exist?(SPEC::TMPDIR)
+  end
+  after do
+    FileUtils.rm_rf(SPEC::TMPDIR)
+  end
 
   @srf = Ms::Sequest::Srf.new(SPEC::Srf_file)
 
@@ -169,6 +200,14 @@ describe "programmatic interface srf to sqt" do
 end
 
 describe "command-line interface srf to sqt" do
+  before do
+    FileUtils.mkdir(SPEC::TMPDIR) unless File.exist?(SPEC::TMPDIR)
+  end
+  after do
+    FileUtils.rm_rf(SPEC::TMPDIR)
+  end
+
+
   def commandline_lambda(string)
     lambda { Ms::Sequest::Srf::Sqt.commandline( string.split(/\s+/) ) }
   end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 16
-  version: 0.0.16
+  - 17
+  version: 0.0.17
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,69 +14,101 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-09-02 00:00:00 -06:00
+date: 2011-02-24 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: arrayclass
-  prerelease: false
+  name: ms-core
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 1
         - 0
-        version: 0.1.0
+        - 11
+        version: 0.0.11
   type: :runtime
+  prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: ms-core
-  prerelease: false
+  name: arrayclass
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
         - 0
+        - 1
         - 0
-        - 2
-        version: 0.0.2
+        version: 0.1.0
   type: :runtime
+  prerelease: false
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: ms-fasta
-  prerelease: false
+  name: ms-testdata
   requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 4
         - 1
-        version: 0.4.1
-  type: :runtime
+        - 1
+        version: 0.1.1
+  type: :development
+  prerelease: false
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
-  name: ms-testdata
-  prerelease: false
+  name: spec-more
   requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 18
-        - 0
-        version: 0.18.0
+        version: "0"
   type: :development
+  prerelease: false
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  name: spec-more
-  prerelease: false
+  name: bundler
   requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -84,12 +116,13 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id005
+  prerelease: false
+  version_requirements: *id007
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables: 
-- srf_to_sqt.rb
 - srf_to_search.rb
+- srf_to_sqt.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -97,8 +130,9 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .autotest
-- .gitignore
 - .gitmodules
+- Gemfile
+- Gemfile.lock
 - History
 - LICENSE
 - README.rdoc
@@ -121,7 +155,6 @@ files:
 - spec/ms/sequest/sqt_spec.rb
 - spec/ms/sequest/sqt_spec_helper.rb
 - spec/ms/sequest/srf/search_spec.rb
-- spec/ms/sequest/srf/search_spec_helper.rb
 - spec/ms/sequest/srf/sqt_spec.rb
 - spec/ms/sequest/srf_spec.rb
 - spec/ms/sequest/srf_spec_helper.rb
@@ -135,21 +168,24 @@ files:
 - spec/testfiles/small2.sqt
 has_rdoc: true
 homepage: http://github.com/jtprince/ms-sequest
-licenses: []
-
+licenses: 
+- MIT
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 1512994769580445168
       segments: 
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -159,19 +195,18 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: mspire
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
 test_files: 
-- spec/ms/sequest/srf_spec_helper.rb
-- spec/ms/sequest/pepxml_spec.rb
 - spec/ms/sequest/bioworks_spec.rb
-- spec/ms/sequest/srf/search_spec.rb
-- spec/ms/sequest/srf/search_spec_helper.rb
-- spec/ms/sequest/srf/sqt_spec.rb
-- spec/ms/sequest/sqt_spec_helper.rb
 - spec/ms/sequest/params_spec.rb
+- spec/ms/sequest/pepxml_spec.rb
 - spec/ms/sequest/sqt_spec.rb
+- spec/ms/sequest/sqt_spec_helper.rb
+- spec/ms/sequest/srf/search_spec.rb
+- spec/ms/sequest/srf/sqt_spec.rb
 - spec/ms/sequest/srf_spec.rb
+- spec/ms/sequest/srf_spec_helper.rb
 - spec/spec_helper.rb

data/.gitignore

@@ -1,8 +0,0 @@
-.DS_Store
-pkg/
-rdoc/
-backup/
-config/
-data/
-*.swp
-*.gemspec

data/spec/ms/sequest/srf/search_spec_helper.rb

@@ -1,341 +0,0 @@
-class SRF_TO_MGF_HELPER
-  FIRST_MSMS = <<FINISH
-BEGIN IONS
-TITLE=000.2.2.1.dta
-CHARGE=1+
-PEPMASS=391.04541015625
-111.976043701172 41418.0
-112.733383178711 88292.0
-113.536590576172 26129.0
-149.049530029297 2852380.0
-149.960266113281 110104.0
-150.578399658203 4607.0
-155.026885986328 16524.0
-160.48388671875 17154.0
-161.9013671875 6562.0
-164.386596679688 76498.0
-166.8427734375 1663866.0
-167.719482421875 72010.0
-168.693237304688 57081.0
-197.131774902344 7933.0
-217.975738525391 20193.0
-218.799468994141 15350.0
-222.215576171875 21254.0
-223.027404785156 27495.0
-224.90771484375 16117.0
-225.895538330078 25061.0
-253.583435058594 7431.0
-255.372528076172 25846.0
-257.151245117188 5435.0
-258.856323242188 26408.0
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-END IONS
-
-FINISH
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-LAST_MSMS = <<FINISH
-BEGIN IONS
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-CHARGE=3+
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-FINISH
-end
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-class SRF_TO_DTA_HELPER
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-LAST_SCAN = <<FINISH
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-FINISH
-end