fixed paths in assemble_seq_idba + velvet

[biopieces.git] / bp_bin / assemble_seq_velvet

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index c3e25f35e35119b582ceaef72baa8bdee1142280..08629852c921b42ed75011879489e6a771520a9e 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -45,7 +45,7 @@ class Velvet
     kmer = @kmer_min
 
     while kmer <= @kmer_max
-      dir_velveth = [@directory, "Kmer_#{kmer}"].join(File::SEPARATOR)
+      dir_velveth = File.join(@directory, "Kmer_#{kmer}")
 
       Dir.mkdir(dir_velveth)
 
@@ -68,7 +68,7 @@ class Velvet
       files_velveth = Dir.glob("#{dir_velveth}/*")
 
       cov_cutoffs.each do |cov_cutoff|
-        dir_velvetg = [dir_velveth, "Cov_cutoff_#{cov_cutoff}"].join(File::SEPARATOR)
+        dir_velvetg = File.join(dir_velveth, "Cov_cutoff_#{cov_cutoff}")
 
         Dir.mkdir(dir_velvetg)
         FileUtils.cp_r files_velveth, dir_velvetg
@@ -160,7 +160,7 @@ raise ArgumentError, "kmer_min >= kmer_max: #{options[:kmer_min]} >= #{options[:
 
 Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 
-file_fasta = [options[:directory], "sequence_in.fna"].join(File::SEPARATOR)
+file_fasta = File.join(options[:directory], "sequence_in.fna")
 
 Fasta.open(file_fasta, mode="w") do |fasta_io|
   bp.each_record do |record|