mspire 0.3.0 → 0.3.1

data/Rakefile

@@ -238,7 +238,7 @@ spec = Gem::Specification.new do |s|
   s.rdoc_options = rdoc_options
   s.extra_rdoc_files = rdoc_extra_includes
   s.executables = FL["bin/*"].map {|file| File.basename(file) }
-  s.add_dependency('libjtp', '~> 0.2.5')
+  s.add_dependency('libjtp', '~> 0.2.12')
   s.add_dependency('axml')
   s.requirements << '"libxml" is the prefered xml parser right now.  libxml, xmlparser, REXML and regular expressions are used as fallback in some routines.'
   s.requirements << 'some plotting functions will not be available without the "gnuplot" gem (and underlying gnuplot binary)'

data/changelog.txt

@@ -122,3 +122,7 @@ interfaces and implementations (using ArrayClass)
 
 1. IMPORTANT BUG FIX: protein reporting in srf files is correct now (proteins after the first protein were being assigned to the last hit in an out file).
 2. SQT export is correct and works at least on 3.2 and 3.3.1.
+
+## version 0.3.1
+
+1. Bug fix in srf filtering (num_hits adjusted)

data/lib/mspire.rb

@@ -1,4 +1,4 @@
 
 module Mspire
-  Version = '0.3.0'
+  Version = '0.3.1'
 end

data/lib/spec_id/sequest/pepxml.rb

@@ -411,7 +411,7 @@ Default_Options = {
         if second_hit ; '0'
         else ; '1'
         end
-       
+
       ## mass calculations:
       precursor_neutral_mass = dta_file.mh - h_plus
       calc_neutral_pep_mass = top_hit[0] - h_plus

data/lib/spec_id/srf.rb

@@ -130,6 +130,7 @@ class SRFGroup
         end
         if hits.size != before
           SRF::OUT::Pep.set_deltacn_from_xcorr(hits)
+          out_file.num_hits = hits.size
         end
       end
     end

data/script/tpp_installer.rb

@@ -175,9 +175,9 @@ if ARGV.size < 1
 
   PREREQS:
   sudo apt-get install <prereq>
-    make, g++, ruby, apache2, libzzip-dev, libgd2-dev, libpng3-dev 
+    make, g++, ruby, apache2, libzzip-dev, libgd2-dev, libpng3-dev libexpat-dev 
   --> or all on one line:
-  sudo apt-get install make g++ ruby apache2 libzzip-dev libgd2-dev libpng3-dev
+  sudo apt-get install make g++ ruby apache2 libzzip-dev libgd2-dev libpng3-dev libexpat-dev
 
   In all likelihood, this will need to be run as root.
   "
@@ -224,7 +224,7 @@ Dir.chdir ARGV[0] do
   swap_line(sequest2xml, /cerr << " error: length of " << result->spectrum_ << " less than 13" << endl;/, 'cerr << " error: length of " << result->spectrum_ << " less than 6" << endl;')
   # CLEAN, MAKE, MAKE INSTALL:
   Dir.chdir('src') do
-    #sys "make clean"
+    sys "make clean"
     sys "make all"
     sys "make install"
   end

data/specs/bin/filter_and_validate_spec.rb

@@ -106,7 +106,44 @@ describe 'filter_and_validate.rb on small bioworks file' do
 
     struct = @st_to_yaml.call( "#{@fake_bioworks_file} --proteins  -1 0.0 -2 0.0 -3 0.0 -d 0.01 -p 1000000 --decoy /^DECOY_/ --digestion #{@small_fasta_file},#{@params_file} --bad_aa C,true,0.001 --bad_aa E,true --bad_aa C,false,0.001 --bias #{@small_bias_fasta_file},true --bias #{@small_bias_fasta_file},false --bias #{@small_bias_fasta_file},true,0.2 --tmm #{@phobius_file},1,true,0.8,0.2 --tmm #{@phobius_file} --tmm #{@toppred_file},3,true,false --tmm #{@toppred_file} --tps #{@small_bias_fasta_file} -o text_table:#{@table_output_file} " )
     frozen = YAML.load_file( File.dirname(__FILE__) + "/filter_and_validate__multiple_vals_helper.yaml" )
-    struct.should == frozen
+
+    ## Pephits precision:
+    ordering = frozen['pephits_precision'].map {|v| v['validator'] }
+    vals = frozen['pephits_precision'].map {|v| v['value'] }
+    struct['pephits_precision'].zip(ordering, vals) do |act, vali, val|
+      act['validator'].should == vali
+      act['value'].should == val
+    end
+
+    struct['pephits'].should == frozen['pephits']
+
+    ##### Params:
+    frp = frozen['params']
+    stp = struct['params']
+
+    frp['validators'].zip(stp['validators']) do |f,s|
+      f.should == s
+    end
+
+    %w(ties prefilter top_hit_by decoy_on_match postfilter include_ties_in_top_hit_postfilter hits_together proteins include_ties_in_top_hit_prefilter).each do |k|
+      stp[k].should == frp[k]
+    end
+    
+    ## digestion & output (special)
+    %w(digestion output).each do |k|
+      stp[k].zip(frp[k]).each do |s,f|
+        File.basename( s.gsub('\\', '/') ).should == File.basename(f)
+      end
+    end
+
+    ## Sequest:
+    frp['sequest'].each do |k,v|
+      stp['sequest'][k].should == v
+    end
+
+    ## TODO: Fill in protein level stuff once stabilized
+
+    #struct.should == frozen
 
     text_table = IO.read(@table_output_file)
 

data/specs/bin/prob_validate_spec.rb

@@ -46,15 +46,22 @@ describe 'filter_and_validate.rb on small bioworks file' do
 
   it 'responds to --prob init' do
     normal = @st_to_yaml.call( @args + " --prob" )
-    normal[:pephits_precision].first[:values].should == [1.0, 1.0, 0.996655518394649, 0.918918918918919]
+
+ normal[:pephits_precision].first[:values].zip([1.0, 1.0, 0.996655518394649, 0.918918918918919]) do |got,exp|
+      got.should be_close(exp, 0.000000000001)
+    end
     #normal_nsp = @st_to_yaml.call( @args + " --prob nsp" )
     #normal.should == normal_nsp
     init = @st_to_yaml.call( @args + " --prob init" )
     init.should_not == normal
-    init[:pephits_precision].first[:values].should == [1.0, 0.974358974358974, 0.981324278438031, 0.890429958391123]
+    init[:pephits_precision].first[:values].zip([1.0, 0.974358974358974, 0.981324278438031, 0.890429958391123]) do |got,exp|
+      got.should be_close(exp, 0.000000000001)
+    end
     with_sort_by = @st_to_yaml.call( @args + " --prob nsp --sort_by_init" )
     # frozen
-    with_sort_by[:pephits_precision].first[:values].should == [1.0, 0.994974874371859, 0.996655518394649, 0.918918918918919]
+    with_sort_by[:pephits_precision].first[:values].zip([1.0, 0.994974874371859, 0.996655518394649, 0.918918918918919]) do |got,exp|
+      got.should be_close(exp, 0.000000000001)
+    end
   end
 
 end

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.2
 specification_version: 1
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.3.0
-date: 2007-12-13 00:00:00 -06:00
+  version: 0.3.1
+date: 2007-12-14 00:00:00 -06:00
 summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
 require_paths: 
 - lib
@@ -368,7 +368,7 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        version: 0.2.5
+        version: 0.2.12
     version: 
 - !ruby/object:Gem::Dependency 
   name: axml