ms-sequest 0.1.1 → 0.1.2

data/History

@@ -1,3 +1,7 @@
+== 0.1.2 / 2011-07-05
+
+* fixed a few bugs caused by newer ms-search
+
 == 0.1.0 / 2011-04-11
 
 * moved Arrayclass objects to Struct objects

data/Rakefile

@@ -11,13 +11,13 @@ Jeweler::Tasks.new do |gem|
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
   gem.rubyforge_project = 'mspire'
-  gem.add_runtime_dependency "ms-ident", ">= 0.0.20"
-  gem.add_runtime_dependency "ms-core", ">= 0.0.17"
+  gem.add_runtime_dependency "ms-ident", ">= 0.1.1"
+  gem.add_runtime_dependency "ms-core", ">= 0.0.19"
   #gem.add_runtime_dependency "ms-msrun", ">= 0.3.4"
-  gem.add_runtime_dependency "trollop", "~> 1.16"
+  gem.add_runtime_dependency "trollop", "~> 1.16.2"
   gem.add_development_dependency "jeweler", "~> 1.5.2"
   gem.add_development_dependency "ms-testdata", ">= 0.1.1"
-  gem.add_development_dependency "spec-more", ">= 0"
+  gem.add_development_dependency "spec-more", ">= 0.0.4"
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/lib/ms/sequest/sqt.rb

@@ -54,8 +54,7 @@ module Ms
     end # SqtGroup
 
 
-    class Sqt
-      include Ms::Ident::Search
+    class Sqt < Ms::Ident::Search
       PercolatorHeaderMatch = /^Percolator v/
         Delimiter = "\t"
       attr_accessor :header

data/lib/ms/sequest/srf.rb

@@ -14,8 +14,7 @@ require 'ms/sequest/params'
 module Ms ; end
 module Ms::Sequest ; end
 
-class Ms::Sequest::Srf
-  include Ms::Ident::Search
+class Ms::Sequest::Srf < Ms::Ident::Search
 
   class NoSequestParamsError < ArgumentError
   end
@@ -102,7 +101,7 @@ class Ms::Sequest::Srf
   #     # will attempt to read peptide hit information (equivalent to .out
   #     # files), otherwise, just reads the dta information.
   def initialize(filename=nil, opts={})
-    @peptides = []
+    @peptide_hits = []
 
     @dta_files = []
     @out_files = []
@@ -270,7 +269,7 @@ class Ms::Sequest::Srf
         outfile.charge = ind[2]
 
         pep_hits = @out_files[i].hits
-        @peptides.push( *pep_hits )
+        @peptide_hits.push( *pep_hits )
         pep_hits.each do |pep_hit|
           pep_hit[15] = @base_name
           pep_hit[16] = ind[0]
@@ -286,7 +285,7 @@ class Ms::Sequest::Srf
       filter_by_precursor_mass_tolerance! if params
 
       if opts[:link_protein_hits]
-        (@peptides, @proteins) = merge!([self.peptides]) do |_protein, _peptides|
+        (@peptide_hits, @proteins) = merge!([self.peptide_hits]) do |_protein, _peptides|
           Ms::Sequest::Srf::Out::Protein.new(_protein.reference, _peptides)
         end
       end
@@ -615,7 +614,7 @@ end
 # deltacn should also be changed to reflect it. 
 # mh - the theoretical mass + h
 # proteins are created as SRF prot objects with a reference and linked to their
-# peptides (from global hash by reference)
+# peptide_hits (from global hash by reference)
 # ppm = 10^6 * ∆m_accuracy / mass_measured  [ where ∆m_accuracy = mass_real – mass_measured ]
 # This is calculated for the M+H mass!
 # num_other_loci is the number of other loci that the peptide matches beyond
@@ -728,7 +727,7 @@ end
 Ms::Sequest::Srf::Out::Protein = Struct.new( *%w(reference peptides).map(&:to_sym) )
 
 class Ms::Sequest::Srf::Out::Protein
-  include Ms::Ident::Protein
+  #include Ms::Ident::Protein
 
   ## we shouldn't have to do this because this is inlcuded in SpecID::Protein, but
   ## under some circumstances it won't work without explicitly calling it.
@@ -741,6 +740,10 @@ class Ms::Sequest::Srf::Out::Protein
   end
   $VERBOSE = tmp
 
+  def first_entry
+    reference.split(/[\s\r]/)[0]
+  end
+
   #  "<Ms::Sequest::Srf::Out::Protein reference=\"#{@reference}\">"
 
   undef_method :inspect

data/lib/ms/sequest/srf/pepxml.rb

@@ -155,24 +155,24 @@ class Ms::Sequest::Srf
         msms_pipeline_analysis.merge!(:summary_xml => summary_xml_filename, :pepxml_version => opt[:pepxml_version]) do |msms_run_summary|
           # prep the sample enzyme and search_summary
           msms_run_summary.merge!(
-            :base_name => File.join(opt[:mz_dir], srf.base_name_noext),
+            { :base_name => File.join(opt[:mz_dir], srf.base_name_noext),
             :ms_manufacturer => opt[:ms_manufacturer],
             :ms_model => opt[:ms_model],
             :ms_ionization => opt[:ms_ionization],
             :ms_mass_analyzer => opt[:ms_mass_analyzer],
             :ms_detector => opt[:ms_detector],
             :raw_data => opt[:raw_data].first,
-            :raw_data_type => opt[:raw_data].first,
+            :raw_data_type => opt[:raw_data].first, }
           ) do |sample_enzyme, search_summary, spectrum_queries|
             sample_enzyme.merge!(params.sample_enzyme_hash)
             sample_enzyme.name = opt[:enzyme] if opt[:enzyme]
             search_summary.merge!(
-              :base_name=> srf.resident_dir + '/' + srf.base_name_noext,
+              { :base_name=> srf.resident_dir + '/' + srf.base_name_noext,
               :search_engine => 'SEQUEST',
               :precursor_mass_type => params.precursor_mass_type,
               :fragment_mass_type => params.fragment_mass_type,
               :out_data_type => opt[:out_data_type],
-              :out_data => opt[:out_data],
+              :out_data => opt[:out_data], }
             ) do |search_database, enzymatic_search_constraint, modifications_ar, parameters_hash|
               search_database.merge!(:local_path => db_filename, :seq_type => opt[:db_seq_type], :database_name => opt[:db_name], :orig_database_url => opt[:db_orig_url], :database_release_date => opt[:db_release_date], :database_release_identifier => opt[:db_release_id])
 
@@ -184,9 +184,9 @@ class Ms::Sequest::Srf
               end
 
               enzymatic_search_constraint.merge!(
-                :enzyme => opt[:enzyme] ? opt[:enzyme] : params.enzyme, 
+                { :enzyme => opt[:enzyme] ? opt[:enzyme] : params.enzyme, 
                 :max_num_internal_cleavages => params.max_num_internal_cleavages,
-                :min_number_termini => params.min_number_termini,
+                :min_number_termini => params.min_number_termini, }
               )
               modifications_ar.replace(modifications_obj.modifications)
               parameters_hash.merge!(params.opts)
@@ -240,10 +240,10 @@ class Ms::Sequest::Srf
                   end
                 end
               Ms::Ident::Pepxml::SpectrumQuery.new(
-                :spectrum  => [srf.base_name_noext, *i_ar].join('.'), :start_scan => i_ar[0], :end_scan => i_ar[1], 
+                { :spectrum  => [srf.base_name_noext, *i_ar].join('.'), :start_scan => i_ar[0], :end_scan => i_ar[1], 
                 :precursor_neutral_mass => dta_file.mh - h_plus, :assumed_charge => i_ar[2],
                 :retention_time_sec => ret_time,  
-                :search_results => [sr], 
+                :search_results => [sr], }
               )
             end
             spectrum_queries.replace(spec_queries)

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

@@ -1,5 +1,6 @@
 require 'spec_helper'
 
+require 'stringio'
 require 'ms/sequest/srf'
 require 'ms/sequest/srf/sqt'
 

metadata

@@ -2,7 +2,7 @@
 name: ms-sequest
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors: 
 - John T. Prince
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-12 00:00:00 -06:00
+date: 2011-07-05 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -21,7 +21,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.0.20
+        version: 0.1.1
   type: :runtime
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
@@ -32,7 +32,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.0.17
+        version: 0.0.19
   type: :runtime
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
@@ -43,7 +43,7 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        version: "1.16"
+        version: 1.16.2
   type: :runtime
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
@@ -76,7 +76,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: "0"
+        version: 0.0.4
   type: :development
   version_requirements: *id006
 description: reads .SRF, .SQT and supports conversions
@@ -161,16 +161,5 @@ rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
-test_files: 
-- spec/ms/sequest/bioworks_spec.rb
-- spec/ms/sequest/params_spec.rb
-- spec/ms/sequest/pepxml/modifications_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/pepxml_spec.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
+test_files: []
+