lib/ms/in_silico/digest.rb in ms-in_silico-0.2.2 vs lib/ms/in_silico/digest.rb in ms-in_silico-0.2.3

@@ -3,30 +3,47 @@
 module Ms
   module InSilico
     # Ms::InSilico::Digest::manifest digest a protein sequence into peptides
     # Digest a protein sequence into an array of peptides.
     #
-    #   % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --: dump --no-audit
+    #   % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --:i dump
     #     I[14:37:55]             digest MIVIGRSIVHP... to 3 peptides
-    #   # date: 2008-09-15 14:37:55
-    #   ---
-    #   ms/in_silico/digest (23483900):
-    #   - - MIVIGR
-    #     - SIVHPYITNEYEPFAAEK
-    #     - QQILSIMAG
+    #   MIVIGR
+    #   SIVHPYITNEYEPFAAEK
+    #   QQILSIMAG
     #
     class Digest < Tap::Task
     
-      config :digester, 'Trypsin'              # the name of the digester
-      config :max_misses, 0, &c.integer        # the max # of missed cleavage sites
-      config :site_digest, false, &c.boolean   # digest to sites (rather than sequences)
-      
+      config :digester, 'Trypsin'                # The name of the digester
+      config :min_length, nil, &c.integer_or_nil # Minimum peptide length
+      config :max_length, nil, &c.integer_or_nil # Maximum peptide length
+      config :max_misses, 0, &c.integer          # The max # of missed cleavage sites
+      config :site_digest, false, &c.boolean     # Digest to sites (rather than sequences)
+
       def process(sequence)
         unless d = Digester[digester]
           raise ArgumentError, "unknown digester: #{digester}" 
         end
         
-        peptides = site_digest ? d.site_digest(sequence, max_misses): d.digest(sequence, max_misses)
+        # extract sequence from FASTA entries
+        sequence = $1 if sequence =~ /\A>.*?\n(.*)\z/m
+        sequence.gsub!(/\s/, "")
+        
+        peptides = if site_digest 
+          d.site_digest(sequence, max_misses)
+        else
+          d.digest(sequence, max_misses)
+        end
+        
+        # filter
+        peptides.delete_if do |peptide|
+          peptide.length < min_length
+        end if min_length
+        
+        peptides.delete_if do |peptide|
+          peptide.length > max_length
+        end if max_length
+        
         log 'digest', "#{sequence[0..10]}#{sequence.length > 10 ? '...' : ''} to #{peptides.length} peptides"
         peptides
       end
       
     end 
\ No newline at end of file