mspire-sequest 0.2.5

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

@@ -0,0 +1,218 @@
+require 'mspire/sequest'
+require 'mspire/sequest/srf'
+require 'mspire/sequest/sqt'
+
+
+module Mspire
+  module Sequest
+    class Srf
+      
+      module Sqt
+
+        # 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] + 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.sub(/\.hdr$/, '') # remove the .hdr postfix
+          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' => Mspire::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 = Mspire::Sequest::Sqt.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 = 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")
+              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 = 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")
+                hit.proteins.each do |prot|
+                  out.puts ['L', prot.first_entry].join("\t")
+                end
+              end
+            end
+          end # close the filehandle
+        end # method
+      end # Sqt
+      include Sqt
+    end # Srf
+  end # Sequest
+end # MS
+
+
+require 'optparse'
+
+module Mspire::Sequest::Srf::Sqt
+  def self.commandline(argv, progname=$0)
+    opt = {
+      :filter => true
+    }
+    opts = OptionParser.new do |op|
+      op.banner = "usage: #{progname} [OPTIONS] <file>.srf ..."
+      op.separator "output: <file>.sqt ..."
+      op.separator ""
+      op.separator "options:"
+      op.on("-d", "--db-info", "calculates num aa's and md5sum on db") {|v| opt[:db_info] = v }
+      op.on("-p", "--db-path <String>", "If you need to specify the database path") {|v| opt[:new_db_path] = v }
+      op.on("-u", "--db-update", "update the sqt file to reflect --db_path") {|v| opt[:db_update] = v }
+      op.on("-n", "--no-filter", "by default, pephit must be within peptide_mass_tolerance",  "(defined in sequest.params) to be included.  Turns this off.") { opt[:filter] = false }
+      op.on("-o", "--outfiles <first,...>", Array, "Comma list of output filenames") {|v| opt[:outfiles] = v }
+      op.on("-r", "--round", "round floating point values reasonably") {|v| opt[:round] = v }
+    end
+    opts.parse!(argv)
+
+    if argv.size == 0
+      puts(opts) || exit
+    end
+
+    if opt[:outfiles] && (opt[:outfiles].size != argv.size)
+      raise "if outfiles specified, outfiles must be same size as number of input files"
+    end
+
+    argv.each_with_index do |srf_file,i|
+      outfile = 
+        if opt[:outfiles]
+          opt[:outfiles][i]
+        else
+          base = srf_file.chomp(File.extname(srf_file))
+          base + '.sqt'
+        end
+
+      srf = Mspire::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
+end
+
+