ms-in_silico 0.2.2 → 0.2.3

data/History

@@ -1,3 +1,10 @@
+== 0.2.3 / 2009-03-31
+
+* Digest now allows fasta entry inputs
+* added min/max length filters to digest
+* Digest removes whitespace from sequence
+* updates for latest Tap
+
 == 0.2.2 / 2009-02-24
 
 * updated return value of Fragment

data/lib/ms/in_silico/digest.rb

@@ -5,27 +5,44 @@ module Ms
     # 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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ms-in_silico
 version: !ruby/object:Gem::Version 
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-02-24 00:00:00 -07:00
+date: 2009-03-31 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -20,7 +20,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.12.0
+        version: 0.12.4
     version: 
 - !ruby/object:Gem::Dependency 
   name: molecules