removed name option from asseble_seq_idba

[biopieces.git] / bp_bin / assemble_seq_velvet

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index cf6160f05ede5477b57c6f366d88cfad05686ae6..557aa569e88c09562f2f33fa7f879b14dd6f4b81 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -46,7 +46,7 @@ class Velvet
     kmer = @kmer_min
 
     while kmer <= @kmer_max
-      dir_velveth = [@directory, "Velvet_#{kmer}"].join(File::SEPARATOR)
+      dir_velveth = [@directory, "Kmer_#{kmer}"].join(File::SEPARATOR)
 
       Dir.mkdir(dir_velveth)
 
@@ -65,7 +65,7 @@ class Velvet
   end
 
   def run_velvetg(cov_cutoffs, exp_cov)
-    Dir.glob("#{@directory}/Velvet_*").each do |dir_velveth|
+    Dir.glob("#{@directory}/Kmer_*").each do |dir_velveth|
       files_velveth = Dir.glob("#{dir_velveth}/*")
 
       cov_cutoffs.each do |cov_cutoff|
@@ -79,6 +79,7 @@ class Velvet
         commands << dir_velvetg
         commands << "-cov_cutoff #{cov_cutoff}"
         commands << "-exp_cov #{exp_cov}"
+        commands << "-clean yes"
 
         execute(commands)
       end
@@ -88,7 +89,7 @@ class Velvet
   def pick_best_assembly
     list = []
 
-    Dir.glob("#{@directory}/Velvet_*/Cov_cutoff_*/contigs.fa").each do |file|
+    Dir.glob("#{@directory}/Kmer_*/Cov_cutoff_*/contigs.fa").each do |file|
       n50 = fasta_n50(file)
       list << [file, n50]
     end