set cutoff to auto in velvet

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2064 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 98c0ba4486a23d47b6969cd9d56d2a4e1902f24b..90cf759b8c82c6fd947c6356a85961c2b20e2c19 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -63,25 +63,23 @@ class Velvet
     end
   end
 
-  def run_velvetg(cov_cutoffs, exp_cov)
+  def run_velvetg(cov_cutoff, exp_cov)
     Dir.glob("#{@directory}/Kmer_*").each do |dir_velveth|
       files_velveth = Dir.glob("#{dir_velveth}/*")
 
-      cov_cutoffs.each do |cov_cutoff|
-        dir_velvetg = File.join(dir_velveth, "Cov_cutoff_#{cov_cutoff}")
+      dir_velvetg = File.join(dir_velveth, "Cov_cutoff_#{cov_cutoff}")
 
-        Dir.mkdir(dir_velvetg)
-        FileUtils.cp_r files_velveth, dir_velvetg
-        
-        commands = []
-        commands << "velvetg"
-        commands << dir_velvetg
-        commands << "-cov_cutoff #{cov_cutoff}"
-        commands << "-exp_cov #{exp_cov}"
-        commands << "-clean yes"
+      Dir.mkdir(dir_velvetg)
+      FileUtils.cp_r files_velveth, dir_velvetg
+      
+      commands = []
+      commands << "velvetg"
+      commands << dir_velvetg
+      commands << "-cov_cutoff #{cov_cutoff}"
+      commands << "-exp_cov #{exp_cov}"
+      commands << "-clean yes"
 
-        execute(commands)
-      end
+      execute(commands)
     end
   end
 
@@ -139,16 +137,15 @@ class Velvet
 end
 
 types       = 'short,shortPaired,long,longPaired'
-cov_cutoffs = "2,4,8,16"
 
 casts = []
-casts << {:long=>'directory',  :short=>'d', :type=>'dir',    :mandatory=>true,  :default=>nil,         :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'type',       :short=>'t', :type=>'string', :mandatory=>true,  :default=>'short',     :allowed=>types, :disallowed=>nil}
-casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>true,  :default=>19,          :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint',   :mandatory=>true,  :default=>31,          :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list',   :mandatory=>true,  :default=>cov_cutoffs, :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',      :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'clean',      :short=>'X', :type=>'flag',   :mandatory=>false, :default=>nil,         :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'directory',  :short=>'d', :type=>'dir',    :mandatory=>true,  :default=>nil,     :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'type',       :short=>'t', :type=>'string', :mandatory=>true,  :default=>'short', :allowed=>types, :disallowed=>nil}
+casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>true,  :default=>19,      :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint',   :mandatory=>true,  :default=>31,      :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'cov_cutoff', :short=>'c', :type=>'float',  :mandatory=>true,  :default=>'auto',  :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',  :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'clean',      :short=>'X', :type=>'flag',   :mandatory=>false, :default=>nil,     :allowed=>nil,   :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)