ms-mascot 0.1.0 → 0.2.0

data/lib/ms/mascot/predict.rb

@@ -1,94 +0,0 @@
-require 'ms/in_silico/digest'
-require 'ms/mascot/fragment'
-require 'ms/mascot/mgf/archive'
-
-module Ms
-  module Mascot
-
-    # Ms::Mascot::Predict::manifest predicts the spectra for a protein sequence
-    #
-    # Fragments a protein sequence and calculates the fragment spectra for
-    # each peptide.  The peptide spectra are formatted as mgf and dumped to
-    # the target. 
-    #
-    #   % rap predict MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFS
-    #     I[16:30:19]             digest MAEELVLERCD... to 15 peptides
-    #     I[16:30:19]           fragment MAEELVLER
-    #     I[16:30:19]           fragment MAEELVLERCDLELETNGR
-    #     I[16:30:19]           fragment CDLELETNGR
-    #     I[16:30:19]           fragment CDLELETNGRDHHTADLCR
-    #     I[16:30:19]           fragment DHHTADLCR
-    #     I[16:30:19]           fragment DHHTADLCREK
-    #     I[16:30:19]           fragment EKLVVR
-    #     I[16:30:19]           fragment LVVR
-    #     I[16:30:19]           fragment LVVRR
-    #     I[16:30:19]           fragment RGQPFWLTLHFEGR
-    #     I[16:30:19]           fragment GQPFWLTLHFEGR
-    #     I[16:30:19]           fragment GQPFWLTLHFEGRNYEASVDSLTFS
-    #     I[16:30:19]           fragment NYEASVDSLTFS
-    #
-    class Predict < Tap::FileTask
-      define :digest, InSilico::Digest, {:max_misses => 1}
-      define :fragment, Mascot::Fragment, {:intensity => 1, :unmask => true, :sort => true}
-      
-      config :headers, nil, &c.hash_or_nil        # a hash of headers to include
-      config :min_length, 3, &c.integer_or_nil    # the minimum peptide length
-      config :mz_precision, 6, &c.integer         # the precision of mzs
-      config :intensity_precision, 0, &c.integer  # the precision of intensities
-      config :pepmass_precision, 6, &c.integer    # the precision of peptide mass
-      
-      # Sequences digest and fragment.  When fragment completes, it will add
-      # a new mgf entry to the internal entries collection.
-      def workflow
-        digest.on_complete do |_results|
-          _results._iterate.each do |_result|
-            next if min_length && _result._current.length < min_length
-            fragment._execute(_result)
-          end
-        end
-     
-        fragment.on_complete do |_result|
-          parent_ion_mass, data = _result._current
-          next if data.empty?
-          
-          peptide = _result._values[-2]
-          headers = {
-            'TITLE' => "#{peptide} (#{fragment.series.join(', ')})",
-            'CHARGE' => fragment.charge,
-            'PEPMASS' => parent_ion_mass}
-          
-          @entries << Mgf::Entry.new(headers, data) 
-        end
-      end
-      
-      # Infers a default path for the output mgf file from the sequence; the 
-      # path is the sequence if the sequence is less than 10 characters,
-      # otherwise it's like: "<first five>_<last five>.mgf"
-      #
-      def default_path(sequence)
-        sequence = "#{sequence[0,5]}_#{sequence[-5,5]}" if sequence.length > 10
-        "#{sequence}.mgf"
-      end
-      
-      def process(sequence, target=nil)
-        sequence = sequence.gsub(/\s/, "")
-        
-        @entries = []
-        digest.execute(sequence)
-        
-        # prepare and dump the predicted spectra
-        # to the target path.
-        target = default_path(sequence) if target == nil
-        prepare(target)
-        File.open(target, "wb") do |file|
-          @entries.each do |entry|
-            entry.dump(file, config)
-            file.puts 
-          end
-        end
-        
-        target
-      end
-    end 
-  end
-end