cleanup of uclust_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1102 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/uclust_seq b/bp_bin/uclust_seq
index 36e40ad19951077eec267a1436c1457cc6d112d8..01dc8da0b0860583433826aaf102cd3a43fa1ddc 100755 (executable)
--- a/bp_bin/uclust_seq
+++ b/bp_bin/uclust_seq
@@ -56,7 +56,6 @@ class Uclust
     # uclust --ublast query_seqs.fasta --db database.fasta --blast6out filename --evalue E
     @options[:e_val] = 10 if @options[:e_val].is_nil?
     @command << "uclust --ublast #{@infile} --db #{@options[:database]} --uc #{@outfile} --evalue #{@options[:e_val]}"
-               @command << "--gapopen *I" if @options.has_key? :no_gaps
 
                execute
   end
@@ -66,7 +65,6 @@ class Uclust
     # uclust --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
     @command << "uclust --query #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
     @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
-               @command << "--gapopen *I" if @options.has_key? :no_gaps
 
                execute
   end
@@ -75,7 +73,6 @@ class Uclust
   def uclust
     # uclust --input seqs_sorted.fasta --uc results.uc --id 0.90
     @command << "uclust --input #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
-               @command << "--gapopen *I" if @options.has_key? :no_gaps
 
                execute
   end
@@ -85,23 +82,10 @@ class Uclust
     # uclust --input seqs_sorted.fasta --lib db.fasta --uc results.uc --id 0.90
     @command << "uclust --input #{@infile} --lib #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
     @command << "--lib #{@options[:database]}" if @options.has_key? :database
-               @command << "--gapopen *I" if @options.has_key? :no_gaps
 
                execute
   end
 
-       # Method to execute a command using a system() call.
-       # The command is composed of bits from the @command variable.
-       def execute
-               @command.unshift "nice -n 19"
-               @command << "> /dev/null 2>&1" unless @options[:verbose]
-               command = @command.join(" ")
-    system(command)
-    raise "Command failed: #{command}" unless $?.success?
-
-               @command = []
-       end
-
        # Method to parse a Uclust .uc file and for each line of data
        # yield a Biopiece record.
   def each
@@ -131,6 +115,20 @@ class Uclust
 
     self # conventionally
   end
+
+  private
+
+       # Method to execute a command using a system() call.
+       # The command is composed of bits from the @command variable.
+       def execute
+               @command.unshift "nice -n 19"
+               @command << "> /dev/null 2>&1" unless @options[:verbose]
+               command = @command.join(" ")
+    system(command)
+    raise "Command failed: #{command}" unless $?.success?
+
+               @command = []
+       end
 end
 
 ok_methods = "ublast,usearch,uclust,usearch_uclust"
@@ -140,7 +138,6 @@ casts << {:long=>'no_sort',  :short=>'n', :type=>'flag',   :mandatory=>false, :d
 casts << {:long=>'method',   :short=>'m', :type=>'string', :mandatory=>true,  :default=>"uclust", :allowed=>ok_methods, :disallowed=>nil}
 casts << {:long=>'database', :short=>'d', :type=>'file!',  :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
 casts << {:long=>'identity', :short=>'i', :type=>'float',  :mandatory=>true,  :default=>0.9,      :allowed=>nil,        :disallowed=>nil}
-casts << {:long=>'no_gaps',  :short=>'g', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
 casts << {:long=>'e_val',    :short=>'e', :type=>'float',  :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
 
 bp = Biopieces.new