ms-sequest 0.0.2

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

@@ -0,0 +1,169 @@
+
+require 'ms/sequest'
+require 'ms/sequest/srf'
+require 'ms/sequest/sqt'
+
+module Ms
+  module Sequest
+    class Srf
+
+      # the out_filename will be the base_name + .sqt unless 'out_filename' is
+      # defined
+      # :round => round floating point numbers
+      # etc...
+      def to_sqt(out_filename=nil, opts={})
+        # default rounding precision (Decimal Places)
+        tic_dp = 2
+        mh_dp = 7
+        xcorr_dp = 5
+        sp_dp = 2
+        dcn_dp = 5
+
+        defaults = {:db_info=>false, :new_db_path=>nil, :update_db_path=>false, :round=>false}
+        opt = defaults.merge(opts)
+
+        outfile =
+          if out_filename
+            out_filename
+          else
+            base_name + '.sqt'
+          end
+        invariant_ordering = %w(SQTGenerator SQTGeneratorVersion Database FragmentMasses PrecursorMasses StartTime) # just for readability and consistency
+        fmt = 
+          if params.fragment_mass_type == 'average' ; 'AVG'
+          else ; 'MONO'
+          end
+        pmt =
+          if params.precursor_mass_type == 'average' ; 'AVG'
+          else ; 'MONO'
+          end
+        
+        mass_index = params.mass_index
+        static_mods = params.static_mods.map do |k,v|
+          key =  k.split(/_/)[1]
+          if key.size == 1
+            key + '=' + (mass_index[key.to_sym] + v.to_f).to_s
+          else
+            key + '=' + v
+          end
+        end
+
+        dynamic_mods = []
+        header.modifications.scan(/\((.*?)\)/) do |match|
+          dynamic_mods << match.first.sub(/ /,'=')
+        end
+        plural = {
+          'StaticMod' => static_mods,
+          'DynamicMod' => dynamic_mods,  # example as diff mod
+          'Comment' => ['Created from Bioworks .srf file']
+        }
+
+
+        db_filename = header.db_filename
+        db_filename_in_sqt = db_filename
+        if opt[:new_db_path]
+          db_filename = File.join(opt[:new_db_path], File.basename(db_filename.gsub('\\', '/')))
+          if opt[:update_db_path]
+            db_filename_in_sqt = File.expand_path(db_filename)
+            warn "writing Database #{db_filename} to sqt, but it does not exist on this file system" unless File.exist?(db_filename) 
+          end
+        end
+
+        apmu = 
+          case params.peptide_mass_units 
+          when '0' : 'amu' 
+          when '1' : 'mmu'
+          when '2' : 'ppm'
+          end
+
+        hh =  {
+          'SQTGenerator' => "mspire: ms-sequest",
+          'SQTGeneratorVersion' => Ms::Sequest::VERSION,
+          'Database' => db_filename_in_sqt,
+          'FragmentMasses' => fmt,
+          'PrecursorMasses' => pmt,
+          'StartTime' => '',  # Bioworks 3.2 also leaves this blank...
+          'Alg-PreMassTol' => params.peptide_mass_tolerance,
+          'Alg-FragMassTol' => params.fragment_ion_tolerance,
+          'Alg-PreMassUnits' => apmu, ## mine
+          'Alg-IonSeries' => header.ion_series.split(':').last.lstrip,
+          'Alg-Enzyme' => header.enzyme.split(':').last,
+          'Alg-MSModel' => header.model,
+        }
+
+        if opt[:db_info]
+          if File.exist?(db_filename)
+            reply = Ms::Sequest::Sqt.get_db_info(db_filename)
+            %w(DBSeqLength DBLocusCount DBMD5Sum).zip(reply) do |label,val|
+              hh[label] = val
+            end
+          else
+            warn "file #{db_filename} does not exist, no extra db info in header!"
+          end
+        end
+
+        has_hits = (self.out_files.size > 0)
+        if has_hits
+          # somewhat redundant with above, but we can get this without a db present!
+          hh['DBLocusCount'] = self.out_files.first.db_locus_count
+        end
+
+        File.open(outfile, 'w') do |out|
+          # print the header:
+          invariant_ordering.each do |iv|
+            out.puts ['H', iv, hh.delete(iv)].join("\t")
+          end
+          hh.each do |k,v|
+            out.puts ['H', k, v].join("\t")
+          end
+          plural.each do |k,vals|
+            vals.each do |val|
+              out.puts ['H', k, val].join("\t")
+            end
+          end
+
+          ##### SPECTRA
+          time_to_process = '0.0'
+          #########################################
+          # NEED TO FIGURE OUT: (in spectra guy)
+          #    * Lowest Sp value for top 500 spectra
+          #    * Number of sequences matching this precursor ion 
+          #########################################
+
+          manual_validation_status = 'U'
+          self.out_files.zip(dta_files) do |out_file, dta_file|
+            # don't have the time to process (using 0.0 like bioworks 3.2)
+            dta_file_mh = dta_file.mh
+            out_file_total_inten = out_file.total_inten
+            out_file_lowest_sp = out_file.lowest_sp
+            if opt[:round]
+              dta_file_mh = round(dta_file_mh, mh_dp)
+              out_file_total_inten = round(out_file_total_inten, tic_dp)
+              out_file_lowest_sp = round(out_file_lowest_sp, 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")
+            out_file.hits.each_with_index do |hit,index|
+              hit_mh = hit.mh
+              hit_deltacn_orig_updated = hit.deltacn_orig_updated
+              hit_xcorr = hit.xcorr
+              hit_sp = hit.sp
+              if opt[:round]
+                hit_mh = round(hit_mh, mh_dp)
+                hit_deltacn_orig_updated = round(hit_deltacn_orig_updated, dcn_dp)
+                hit_xcorr = round(hit_xcorr, xcorr_dp)
+                hit_sp = round(hit_sp, 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")
+              hit.prots.each do |prot|
+                out.puts ['L', prot.first_entry].join("\t")
+              end
+            end
+          end
+        end # close the filehandle
+      end # method
+
+    end # Srf
+  end # Sequest
+end # Ms

metadata

@@ -0,0 +1,88 @@
+--- !ruby/object:Gem::Specification 
+name: ms-sequest
+version: !ruby/object:Gem::Version 
+  version: 0.0.2
+platform: ruby
+authors: 
+- John Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-05-14 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: arrayclass
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.1.0
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: ms-core
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.0.1
+    version: 
+description: 
+email: jtprince@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README
+- MIT-LICENSE
+- History
+files: 
+- lib/ms/sequest/params.rb
+- lib/ms/sequest/srf/sqt.rb
+- lib/ms/sequest/srf.rb
+- lib/ms/sequest/sqt.rb
+- lib/ms/sequest.rb
+- README
+- MIT-LICENSE
+- History
+has_rdoc: true
+homepage: http://mspire.rubyforge.org/projects/ms-sequest/
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --main
+- README
+- -S
+- -N
+- --title
+- Ms-Sequest
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: mspire
+rubygems_version: 1.3.2
+signing_key: 
+specification_version: 3
+summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
+test_files: []
+