search.rb in ms-sequest-0.0.14

- old
+ new
@@ -5,102 +5,152 @@
 # These are for outputting formats used in MS/MS Search engines
 
 module Ms
   module Sequest
     class Srf
-
-      # Writes an MGF file to given filename or base_name + '.mgf' if no
-      # filename given.
-      #
-      # This mimicks the output of merge.pl from mascot The only difference is
-      # that this does not include the "\r\n" that is found after the peak
-      # lists, instead, it uses "\n" throughout the file (thinking that this
-      # is preferable to mixing newline styles!)
-      def to_mgf(filename=nil)
-        filename =
-          if filename ; filename
-          else
-            base_name + '.mgf'
-          end
-        h_plus = Ms::Mass::MASCOT_H_PLUS
-        File.open(filename, 'wb') do |out|
-          dta_files.zip(index) do |dta, i_ar|
-            chrg = dta.charge
-            out.print "BEGIN IONS\n"
-            out.print "TITLE=#{[base_name, *i_ar].push('dta').join('.')}\n"
-            out.print "CHARGE=#{chrg}+\n"
-            out.print "PEPMASS=#{(dta.mh+((chrg-1)*h_plus))/chrg}\n"
-            peak_ar = dta.peaks.unpack('e*')
-            (0...(peak_ar.size)).step(2) do |i|
-              out.print( peak_ar[i,2].join(' '), "\n")
+      module Search
+        # Writes an MGF file to given filename or base_name + '.mgf' if no
+        # filename given.
+        #
+        # This mimicks the output of merge.pl from mascot The only difference is
+        # that this does not include the "\r\n" that is found after the peak
+        # lists, instead, it uses "\n" throughout the file (thinking that this
+        # is preferable to mixing newline styles!)
+        def to_mgf(filename=nil)
+          filename =
+            if filename ; filename
+            else
+              base_name + '.mgf'
             end
-            out.print "END IONS\n"
-            out.print "\n"
+          h_plus = Ms::Mass::MASCOT_H_PLUS
+          File.open(filename, 'wb') do |out|
+            dta_files.zip(index) do |dta, i_ar|
+              chrg = dta.charge
+              out.print "BEGIN IONS\n"
+              out.print "TITLE=#{[base_name, *i_ar].push('dta').join('.')}\n"
+              out.print "CHARGE=#{chrg}+\n"
+              out.print "PEPMASS=#{(dta.mh+((chrg-1)*h_plus))/chrg}\n"
+              peak_ar = dta.peaks.unpack('e*')
+              (0...(peak_ar.size)).step(2) do |i|
+                out.print( peak_ar[i,2].join(' '), "\n")
+              end
+              out.print "END IONS\n"
+              out.print "\n"
+            end
           end
         end
-      end
 
-      # not given an out_folder, will make one with the basename
-      # compress may be: :zip, :tgz, or nil (no compression)
-      # :zip requires gem rubyzip to be installed and is *very* bloated
-      # as it writes out all the files first!
-      # :tgz requires gem archive-tar-minitar to be installed
-      def to_dta(out_folder=nil, compress=nil)
-        outdir = 
-          if out_folder ; out_folder
-          else base_name
-          end
+        # not given an out_folder, will make one with the basename
+        # compress may be: :zip, :tgz, or nil (no compression)
+        # :zip requires gem rubyzip to be installed and is *very* bloated
+        # as it writes out all the files first!
+        # :tgz requires gem archive-tar-minitar to be installed
+        def to_dta(out_folder=nil, compress=nil)
+          outdir = 
+            if out_folder ; out_folder
+            else base_name
+            end
 
-        case compress
-        when :tgz
-          begin
-            require 'archive/tar/minitar'
-          rescue LoadError
-            abort "need gem 'archive-tar-minitar' installed' for tgz compression!\n#{$!}"
-          end
-          require 'archive/targz'  # my own simplified interface!
-          require 'zlib'
-          names = index.map do |i_ar|
-            [outdir, '/', [base_name, *i_ar].join('.'), '.dta'].join('')
-          end
-          #Archive::Targz.archive_as_files(outdir + '.tgz', names, dta_file_data)
+          case compress
+          when :tgz
+            begin
+              require 'archive/tar/minitar'
+            rescue LoadError
+              abort "need gem 'archive-tar-minitar' installed' for tgz compression!\n#{$!}"
+            end
+            require 'archive/targz'  # my own simplified interface!
+            require 'zlib'
+            names = index.map do |i_ar|
+              [outdir, '/', [base_name, *i_ar].join('.'), '.dta'].join('')
+            end
+            #Archive::Targz.archive_as_files(outdir + '.tgz', names, dta_file_data)
 
-          tgz = Zlib::GzipWriter.new(File.open(outdir + '.tgz', 'wb'))
+            tgz = Zlib::GzipWriter.new(File.open(outdir + '.tgz', 'wb'))
 
-          Archive::Tar::Minitar::Output.open(tgz) do |outp|
-            dta_files.each_with_index do |dta_file, i|
-              Archive::Tar::Minitar.pack_as_file(names[i], dta_file.to_dta_file_data, outp)
+            Archive::Tar::Minitar::Output.open(tgz) do |outp|
+              dta_files.each_with_index do |dta_file, i|
+                Archive::Tar::Minitar.pack_as_file(names[i], dta_file.to_dta_file_data, outp)
+              end
             end
-          end
-        when :zip
-          begin
-            require 'zip/zipfilesystem'
-          rescue LoadError
-            abort "need gem 'rubyzip' installed' for zip compression!\n#{$!}"
-          end
-          #begin ; require 'zip/zipfilesystem' ; rescue LoadError, "need gem 'rubyzip' installed' for zip compression!\n#{$!}" ; end
-          Zip::ZipFile.open(outdir + ".zip", Zip::ZipFile::CREATE) do |zfs|
-            dta_files.zip(index) do |dta,i_ar|
-              #zfs.mkdir(outdir)
-              zfs.get_output_stream(outdir + '/' + [base_name, *i_ar].join('.') + '.dta') do |out|
-                dta.write_dta_file(out)
-                #zfs.commit
+          when :zip
+            begin
+              require 'zip/zipfilesystem'
+            rescue LoadError
+              abort "need gem 'rubyzip' installed' for zip compression!\n#{$!}"
+            end
+            #begin ; require 'zip/zipfilesystem' ; rescue LoadError, "need gem 'rubyzip' installed' for zip compression!\n#{$!}" ; end
+            Zip::ZipFile.open(outdir + ".zip", Zip::ZipFile::CREATE) do |zfs|
+              dta_files.zip(index) do |dta,i_ar|
+                #zfs.mkdir(outdir)
+                zfs.get_output_stream(outdir + '/' + [base_name, *i_ar].join('.') + '.dta') do |out|
+                  dta.write_dta_file(out)
+                  #zfs.commit
+                end
               end
             end
-          end
-        else  # no compression
-          FileUtils.mkpath(outdir)
-          Dir.chdir(outdir) do
-            dta_files.zip(index) do |dta,i_ar|
-              File.open([base_name, *i_ar].join('.') << '.dta', 'wb') do |out|
-                dta.write_dta_file(out)
+          else  # no compression
+            FileUtils.mkpath(outdir)
+            Dir.chdir(outdir) do
+              dta_files.zip(index) do |dta,i_ar|
+                File.open([base_name, *i_ar].join('.') << '.dta', 'wb') do |out|
+                  dta.write_dta_file(out)
+                end
               end
             end
           end
         end
-      end
+      end # Search
 
+      include Search
+
     end # Srf
   end # Sequest
 end # Ms
 
 
+require 'optparse'
+module Ms::Sequest::Srf::Search
+  def self.commandline(argv, progname=$0)
+    opt = {
+      :format => 'mgf'
+    }
+    opts = OptionParser.new do |op|
+      op.banner = "usage: #{File.basename(__FILE__)} <file>.srf ..."
+      op.separator "outputs: <file>.mgf ..."
+      op.on("-f", "--format <mgf|dta>", "the output format (default: #{opt[:format]})") {|v| opt[:format] = v }
+      op.on("-o", "--outfiles <String,...>", Array, "comma list of output files or directories") {|v| opt[:outfiles] = v }
+    end
+
+    opts.parse!(argv)
+
+    if argv.size == 0
+      puts(opts) || exit
+    end
+
+    format = opt[:format]
+
+    raise "if outfiles specified, needs the same number of files as input files" unless argv.size == opt[:outfiles].size
+
+    argv.each_with_index do |srf_file,i|
+      base = srf_file.sub(/\.srf$/i, '')
+      newfile = 
+        if opt[:outfiles]
+          opt[:outfiles][i]
+        else
+          case format
+          when 'dta'
+            base
+          when 'mgf'
+            base << '.' << format
+          end
+        end
+      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'
+        srf.to_mgf(newfile)
+      when 'dta'
+        srf.to_dta(newfile)
+      end
+    end
+  end
+end