lib/lederhosen/tasks/cluster.rb in lederhosen-0.5.7 vs lib/lederhosen/tasks/cluster.rb in lederhosen-1.0.0

@@ -1,58 +1,46 @@
-##
-# FINALLY, CLUSTER!
-#
-
 module Lederhosen
+
   class CLI
 
-    desc "cluster",
-         "cluster a fasta file using UCLUST"
+    desc 'cluster', 'reference-based clustering using usearch'
 
-    method_option :input,       :type => :string,  :required => true
-    method_option :output,      :type => :string,  :required => true
-    method_option :identity,    :type => :numeric, :required => true
-    method_option :stepwords,   :type => :numeric, :default  => 8
-    method_option :wordlen,     :type => :numeric, :default  => 8
-    method_option :maxaccepts,  :type => :numeric, :default  => 1
-    method_option :maxrejects,  :type => :numeric, :default  => 8
-    method_option :lib,         :type => :string
-    method_option :libonly,     :type => :boolean, :default  => false
+    method_option :input,    :type => :string,  :required => true
+    method_option :database, :type => :string,  :required => true
+    method_option :threads,  :type => :numeric, :default  => 0
+    method_option :identity, :type => :numeric, :required => true
+    method_option :output,   :type => :string,  :required => true
+    method_option :strand,   :type => :string,  :default => 'plus'
 
     def cluster
-      identity   = options[:identity]
-      output     = options[:output]
-      input      = options[:input]
-      stepwords  = options[:stepwords]
-      maxaccepts = options[:maxaccepts]
-      maxrejects = options[:maxrejects]
-      wordlen    = options[:wordlen]
-      lib        = options[:lib]
-      libonly    = options[:libonly]
+      input    = options[:input]
+      database = options[:database]
+      threads  = options[:threads]
+      identity = options[:identity]
+      output   = options[:output]
+      strand   = options[:strand]
 
-      ohai "clustering #{input}, saving to #{output}"
+      ohai "clustering #{input} to #{database} and saving to #{output}"
 
       options.each_pair do |key, value|
         ohai "#{key} = #{value}"
       end
 
-      cmd = [
-        'uclust',
-        "--input #{input}",
-        "--uc #{output}",
+      cmd = ['usearch',
+        "--usearch_local #{input}",
         "--id #{identity}",
-        "--stepwords #{stepwords}",
-        "--maxaccepts #{maxaccepts}",
-        "--maxrejects #{maxrejects}",
-        "--w #{wordlen}"
+        "--uc #{output}",
+        "--db #{database}",
+        "--strand #{strand}"
       ]
 
-      cmd << "--lib #{lib}" unless lib.nil?
-      cmd << "--libonly" if libonly == true
+      # threads = 0 : use all threads (default)
+      if threads != 0
+        cmd << "--threads #{threads}"
+      end
 
       cmd = cmd.join(' ')
 
-      @shell.mute { run cmd }
+      run cmd
     end
-
   end
 end