ms-sequest 0.1.2 → 0.2.1

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

@@ -1,7 +1,7 @@
-module Ms ; end
-module Ms::Ident ; end
+module MS ; end
+module MS::Ident ; end
 
-class Ms::Ident::Pepxml 
+class MS::Ident::Pepxml 
   class SearchHit
     Sequest = Struct.new(:xcorr, :deltacn, :deltacnstar, :spscore, :sprank) do
 

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

@@ -4,7 +4,7 @@ require 'ms/mass'
 
 # These are for outputting formats used in MS/MS Search engines
 
-module Ms
+module MS
   module Sequest
     class Srf
       module Search
@@ -21,7 +21,7 @@ module Ms
             else
               base_name + '.mgf'
             end
-          h_plus = Ms::Mass::MASCOT_H_PLUS
+          h_plus = MS::Mass::H_PLUS
           File.open(filename, 'wb') do |out|
             dta_files.zip(index) do |dta, i_ar|
               chrg = dta.charge
@@ -104,11 +104,11 @@ module Ms
 
     end # Srf
   end # Sequest
-end # Ms
+end # MS
 
 
 require 'optparse'
-module Ms::Sequest::Srf::Search
+module MS::Sequest::Srf::Search
   def self.commandline(argv, progname=$0)
     opt = {
       :format => 'mgf'
@@ -145,7 +145,7 @@ module Ms::Sequest::Srf::Search
             base << '.' << format
           end
         end
-      srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
+      srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
       # options just speed up reading since we don't need .out info anyway
       case format
       when 'mgf'

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

@@ -1,11 +1,9 @@
-
-require 'ms/calc'
 require 'ms/sequest'
 require 'ms/sequest/srf'
 require 'ms/sequest/sqt'
 
 
-module Ms
+module MS
   module Sequest
     class Srf
       
@@ -81,7 +79,7 @@ module Ms
 
           hh =  {
             'SQTGenerator' => "mspire: ms-sequest",
-            'SQTGeneratorVersion' => Ms::Sequest::VERSION,
+            'SQTGeneratorVersion' => MS::Sequest::VERSION,
             'Database' => db_filename_in_sqt,
             'FragmentMasses' => fmt,
             'PrecursorMasses' => pmt,
@@ -96,7 +94,7 @@ module Ms
 
           if opt[:db_info]
             if File.exist?(db_filename)
-              reply = Ms::Sequest::Sqt.db_info(db_filename)
+              reply = MS::Sequest::Sqt.db_info(db_filename)
               %w(DBSeqLength DBLocusCount DBMD5Sum).zip(reply) do |label,val|
                 hh[label] = val
               end
@@ -140,9 +138,9 @@ module Ms
               out_file_total_inten = out_file.total_inten
               out_file_lowest_sp = out_file.lowest_sp
               if opt[:round]
-                dta_file_mh = Ms::Calc.round(dta_file_mh, mh_dp)
-                out_file_total_inten = Ms::Calc.round(out_file_total_inten, tic_dp)
-                out_file_lowest_sp = Ms::Calc.round(out_file_lowest_sp, sp_dp)
+                dta_file_mh = dta_file_mh.round(mh_dp)
+                out_file_total_inten = out_file_total_inten.round(tic_dp)
+                out_file_lowest_sp = out_file_lowest_sp.round(sp_dp)
               end
 
               out.puts ['S', out_file.first_scan, out_file.last_scan, out_file.charge, time_to_process, out_file.computer, dta_file_mh, out_file_total_inten, out_file_lowest_sp, out_file.num_matched_peptides].join("\t")
@@ -152,10 +150,10 @@ module Ms
                 hit_xcorr = hit.xcorr
                 hit_sp = hit.sp
                 if opt[:round]
-                  hit_mh = Ms::Calc.round(hit_mh, mh_dp)
-                  hit_deltacn_orig_updated = Ms::Calc.round(hit_deltacn_orig_updated, dcn_dp)
-                  hit_xcorr = Ms::Calc.round(hit_xcorr, xcorr_dp)
-                  hit_sp = Ms::Calc.round(hit_sp, sp_dp)
+                  hit_mh = hit_mh.round(mh_dp)
+                  hit_deltacn_orig_updated = hit_deltacn_orig_updated.round(dcn_dp)
+                  hit_xcorr = hit_xcorr.round(xcorr_dp)
+                  hit_sp = hit_sp.round(sp_dp)
                 end
                 # note that the rank is determined by the order..
                 out.puts ['M', index+1, hit.rsp, hit_mh, hit_deltacn_orig_updated, hit_xcorr, hit_sp, hit.ions_matched, hit.ions_total, hit.sequence, manual_validation_status].join("\t")
@@ -170,12 +168,12 @@ module Ms
       include Sqt
     end # Srf
   end # Sequest
-end # Ms
+end # MS
 
 
 require 'optparse'
 
-module Ms::Sequest::Srf::Sqt
+module MS::Sequest::Srf::Sqt
   def self.commandline(argv, progname=$0)
     opt = {
       :filter => true
@@ -211,7 +209,7 @@ module Ms::Sequest::Srf::Sqt
           base + '.sqt'
         end
 
-      srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
+      srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
       srf.to_sqt(outfile, :db_info => opt[:db_info], :new_db_path => opt[:new_db_path], :update_db_path => opt[:db_update], :round => opt[:round])
     end
   end

data/spec/ms/sequest/params_spec.rb

@@ -20,7 +20,7 @@ end
 
 shared 'sequest params' do
   before do
-    @obj = Ms::Sequest::Params.new(@file)
+    @obj = MS::Sequest::Params.new(@file)
   end
 
   it 'has a method for every parameter in the file' do

data/spec/ms/sequest/pepxml/modifications_spec.rb

@@ -3,13 +3,13 @@ require 'spec_helper'
 require 'ms/sequest/params'
 require 'ms/sequest/pepxml/modifications'
 
-describe 'Ms::Sequest::Pepxml::Modifications' do
+describe 'MS::Sequest::Pepxml::Modifications' do
   before do
     tf_params = TESTFILES + "/bioworks32.params"
-    @params = Ms::Sequest::Params.new(tf_params)
+    @params = MS::Sequest::Params.new(tf_params)
     # The params object here is completely unnecessary for this test, except
     # that it sets up the mass table
-    @obj = Ms::Sequest::Pepxml::Modifications.new(@params, "(M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000) ")
+    @obj = MS::Sequest::Pepxml::Modifications.new(@params, "(M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000) ")
   end
   it 'creates a mod_symbols_hash' do
     answ = {[:C, 12.0]=>"^", [:S, 80.0]=>"@", [:M, 29.0]=>"#", [:M, 15.9]=>"*", [:ct, 12.33]=>"[", [:nt, 14.2]=>"]"}
@@ -21,7 +21,7 @@ describe 'Ms::Sequest::Pepxml::Modifications' do
     mod_string = "(M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000) "
     @params.diff_search_options = "15.90000 M 29.00000 M 80.00000 S 12.00000 C"
     @params.term_diff_search_options = "14.20000 12.33000"
-    mod = Ms::Sequest::Pepxml::Modifications.new(@params, mod_string)
+    mod = MS::Sequest::Pepxml::Modifications.new(@params, mod_string)
     ## no mods
     peptide_nomod = "PEPTIDE"
     ok mod.modification_info(peptide_nomod).nil?

data/spec/ms/sequest/sqt_spec.rb

@@ -7,7 +7,7 @@ describe 'reading a small sqt file' do
 
   before do
     file = TESTFILES + '/small.sqt'
-    @sqt = Ms::Sequest::Sqt.new(file)
+    @sqt = MS::Sequest::Sqt.new(file)
   end
 
   it 'can access header entries like a hash' do
@@ -23,7 +23,7 @@ describe 'reading a small sqt file' do
     header.database.is HeaderHash['Database']
     # all working:
     HeaderHash.each do |k,v|
-      header.send(Ms::Sequest::Sqt::Header::KeysToAtts[k]).is v
+      header.send(MS::Sequest::Sqt::Header::KeysToAtts[k]).is v
     end
 
   end
@@ -49,29 +49,3 @@ describe 'reading a small sqt file' do
 
 end
 
-#class SqtGroup_ReadingFiles < MiniTest::Spec
-  #before(:each) do
-    #file1 = TESTFILES + '/small.sqt'
-    #file2 = TESTFILES + '/small2.sqt'
-    #@sqg = Ms::Sequest::SqtGroup.new([file1, file2])
-  #end
-
-  #it 'has peptide hits' do
-    #peps = @sqg.peps
-    #peps.size.is 86
-    ## first hit in 020
-    #peps.first.sequence.is 'R.Y#RLGGS#T#K.K'
-    #peps.first.base_name.is 'small'
-    ## last hit in 040
-    #peps.last.sequence.is 'K.T#IS#S#QK.K'
-    #peps.last.base_name.is 'small2'
-  #end
-
-  #it 'has prots' do
-    ### FROZEN:
-    #@sqg.prots.size.is 72
-    #sorted = @sqg.prots.sort_by {|v| v.reference }
-    #sorted.first.reference.is 'gi|16127996|ref|NP_414543.1|'
-    #sorted.first.peps.size.is 33
-  #end
-#end

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

@@ -2,7 +2,7 @@ require 'spec_helper'
 
 require 'ms/sequest/srf/pepxml'
 
-describe 'an Ms::Ident::Pepxml object from an srf file with modifications' do
+describe 'an MS::Ident::Pepxml object from an srf file with modifications' do
   before do
     FileUtils.mkdir @out_path unless File.exist?(@out_path)
   end
@@ -12,7 +12,7 @@ describe 'an Ms::Ident::Pepxml object from an srf file with modifications' do
 
   @srf_file = SEQUEST_DIR + '/opd1_2runs_2mods/sequest331/020.srf'
   @out_path = TESTFILES + '/tmp'
-  @srf = Ms::Sequest::Srf.new(@srf_file)
+  @srf = MS::Sequest::Srf.new(@srf_file)
 
   it 'produces xml with all the expected parts' do
     tags = %w(msms_pipeline_analysis msms_run_summary sample_enzyme specificity search_summary search_database enzymatic_search_constraint aminoacid_modification parameter spectrum_query search_result search_hit modification_info mod_aminoacid_mass search_score)

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

@@ -12,7 +12,7 @@ class SRF_TO_MGF_HELPER
     :last_line => 'END IONS',
   }
   LAST_MSMS = { 
-    :first_lines => ['BEGIN IONS', 'TITLE=000.3748.3748.3.dta', 'CHARGE=3+', 'PEPMASS=433.56494098625'],
+    :first_lines => ['BEGIN IONS', 'TITLE=000.3748.3748.3.dta', 'CHARGE=3+', 'PEPMASS=433.56494129743004'],
     :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',
@@ -33,7 +33,7 @@ class SRF_TO_DTA_HELPER
   }
 end
 
-Srf_file = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf'
+Srf_file = MS::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf'
 TMPDIR = TESTFILES + '/tmp'
 Mgf_output = TMPDIR + '/000.mgf.tmp'
 Dta_output = TMPDIR + '/000.dta.tmp'
@@ -61,7 +61,7 @@ shared 'an srf to ms2 search converter' do
     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
+    exp_pair.last.to_f.should.be.close act_pair.last.to_f, 0.0000001
 
     (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)
@@ -103,7 +103,7 @@ describe 'converting an srf to ms2 search format: programmatic' do
     FileUtils.rmtree(TMPDIR)
   end
 
-  @srf = Ms::Sequest::Srf.new(Srf_file)
+  @srf = MS::Sequest::Srf.new(Srf_file)
 
   @convert_to_mgf = lambda { @srf.to_mgf(Mgf_output) }
   @convert_to_dta = lambda { @srf.to_dta(Dta_output) }
@@ -121,7 +121,7 @@ describe 'converting an srf to ms2 search format: commandline' do
   end
 
   def commandline_lambda(string)
-    lambda { Ms::Sequest::Srf::Search.commandline(string.split(/\s+/)) }
+    lambda { MS::Sequest::Srf::Search.commandline(string.split(/\s+/)) }
   end
 
   @convert_to_mgf = commandline_lambda "#{Srf_file} -o #{Mgf_output}"

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

@@ -1,6 +1,5 @@
 require 'spec_helper'
 
-require 'stringio'
 require 'ms/sequest/srf'
 require 'ms/sequest/srf/sqt'
 
@@ -47,7 +46,7 @@ END
 
 
 module SPEC
-  Srf_file = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf' 
+  Srf_file = MS::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf' 
   TMPDIR = TESTFILES + '/tmp'
   Srf_output = TMPDIR + '/000.sqt.tmp'
 end
@@ -167,11 +166,11 @@ describe "programmatic interface srf to sqt" do
     FileUtils.rm_rf(SPEC::TMPDIR)
   end
 
-  @srf = Ms::Sequest::Srf.new(SPEC::Srf_file)
+  @srf = MS::Sequest::Srf.new(SPEC::Srf_file)
 
   @basic_conversion = lambda { @srf.to_sqt(SPEC::Srf_output) }
-  @with_new_db_path = lambda { @srf.to_sqt(SPEC::Srf_output, :db_info => true, :new_db_path => Ms::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33') }
-  @update_the_db_path = lambda { @srf.to_sqt(SPEC::Srf_output, :new_db_path => Ms::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33', :update_db_path => true) }
+  @with_new_db_path = lambda { @srf.to_sqt(SPEC::Srf_output, :db_info => true, :new_db_path => MS::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33') }
+  @update_the_db_path = lambda { @srf.to_sqt(SPEC::Srf_output, :new_db_path => MS::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33', :update_db_path => true) }
 
   before do
     @output = SPEC::Srf_output
@@ -210,13 +209,13 @@ describe "command-line interface srf to sqt" do
 
 
   def commandline_lambda(string)
-    lambda { Ms::Sequest::Srf::Sqt.commandline( string.split(/\s+/) ) }
+    lambda { MS::Sequest::Srf::Sqt.commandline( string.split(/\s+/) ) }
   end
 
   base_cmd = "#{SPEC::Srf_file} -o #{SPEC::Srf_output}"
   @basic_conversion = commandline_lambda(base_cmd)
-  @with_new_db_path = commandline_lambda(base_cmd + " --db-info --db-path #{Ms::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33'}")
-  @update_the_db_path = commandline_lambda(base_cmd + " --db-path #{Ms::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33'} --db-update" )
+  @with_new_db_path = commandline_lambda(base_cmd + " --db-info --db-path #{MS::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33'}")
+  @update_the_db_path = commandline_lambda(base_cmd + " --db-path #{MS::TESTDATA + '/sequest/opd1_2runs_2mods/sequest33'} --db-update" )
 
   behaves_like "an srf to sqt converter"
 end

data/spec/ms/sequest/srf_spec.rb

@@ -91,8 +91,8 @@ To_run = {
 describe 'reading srf with duplicate refs v3.2' do
 
   info = To_run['3.2']
-  @file = Ms::TESTDATA + '/sequest' + info[:file]
-  @srf_obj = Ms::Sequest::Srf.new(@file)
+  @file = MS::TESTDATA + '/sequest' + info[:file]
+  @srf_obj = MS::Sequest::Srf.new(@file)
   Expected_hash_keys.each do |c|
     instance_variable_set("@#{c}", info[:hash][c.to_sym])
   end
@@ -102,8 +102,8 @@ end
 
 describe 'reading srf with duplicate refs v3.3' do
   info = To_run['3.3']
-  @file = Ms::TESTDATA + '/sequest' + info[:file]
-  @srf_obj = Ms::Sequest::Srf.new(@file)
+  @file = MS::TESTDATA + '/sequest' + info[:file]
+  @srf_obj = MS::Sequest::Srf.new(@file)
   Expected_hash_keys.each do |c|
     instance_variable_set("@#{c}", info[:hash][c.to_sym])
   end
@@ -113,8 +113,8 @@ end
 
 describe 'reading srf with duplicate refs v3.3.1' do
   info = To_run['3.3.1']
-  @file = Ms::TESTDATA + '/sequest' + info[:file]
-  @srf_obj = Ms::Sequest::Srf.new(@file)
+  @file = MS::TESTDATA + '/sequest' + info[:file]
+  @srf_obj = MS::Sequest::Srf.new(@file)
   Expected_hash_keys.each do |c|
     instance_variable_set("@#{c}", info[:hash][c.to_sym])
   end
@@ -126,7 +126,7 @@ end
 #  it 'reads a file from an aborted run w/o failing, but gives warning msg' do
 #    srf_file = TESTFILES + '/corrupted_900.srf'
 #    message = capture_stderr do
-#      srf_obj = Ms::Sequest::Srf.new(srf_file) 
+#      srf_obj = MS::Sequest::Srf.new(srf_file) 
 #      srf_obj.base_name.is '900'
 #      srf_obj.params.is nil
 #      header = srf_obj.header

data/spec/spec_helper.rb

@@ -16,7 +16,7 @@ def capture_stderr
 end
 
 TESTFILES = File.dirname(__FILE__) + '/testfiles'
-SEQUEST_DIR = Ms::TESTDATA + '/sequest' 
+SEQUEST_DIR = MS::TESTDATA + '/sequest' 
 
 
 Bacon.summary_on_exit

metadata

@@ -2,7 +2,7 @@
 name: ms-sequest
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.1.2
+  version: 0.2.1
 platform: ruby
 authors: 
 - John T. Prince
@@ -10,75 +10,63 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-05 00:00:00 -06:00
-default_executable: 
+date: 2011-09-13 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: ms-ident
+  name: msplat
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.1.1
+        version: 0.0.6
   type: :runtime
   version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: ms-core
-  prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 0.0.19
-  type: :runtime
-  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: trollop
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        version: 1.16.2
+        version: "1.16"
   type: :runtime
-  version_requirements: *id003
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: jeweler
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
         version: 1.5.2
   type: :development
-  version_requirements: *id004
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: ms-testdata
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.1.1
+        version: 0.2.1
   type: :development
-  version_requirements: *id005
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: spec-more
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.0.4
+        version: "0"
   type: :development
-  version_requirements: *id006
+  version_requirements: *id005
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables: 
@@ -102,7 +90,6 @@ files:
 - bin/srf_to_search.rb
 - bin/srf_to_sqt.rb
 - lib/ms/sequest.rb
-- lib/ms/sequest/bioworks.rb
 - lib/ms/sequest/params.rb
 - lib/ms/sequest/pepxml.rb
 - lib/ms/sequest/pepxml/modifications.rb
@@ -114,7 +101,6 @@ files:
 - lib/ms/sequest/srf/search.rb
 - lib/ms/sequest/srf/sqt.rb
 - script/fasta_ipi_to_ncbi-ish.rb
-- 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
@@ -133,7 +119,6 @@ files:
 - spec/testfiles/corrupted_900.srf
 - spec/testfiles/small.sqt
 - spec/testfiles/small2.sqt
-has_rdoc: true
 homepage: http://github.com/jtprince/ms-sequest
 licenses: 
 - MIT
@@ -157,9 +142,19 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: mspire
-rubygems_version: 1.6.2
+rubygems_version: 1.8.5
 signing_key: 
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
-test_files: []
-
+test_files: 
+- 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