fixed paths in assemble_seq_idba + velvet

[biopieces.git] / bp_bin / assemble_seq_idba

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index da2f4dab4d4a0b03e56bce0ee8669954f86eb24b..ef35973f6ea627f1fa280b01d182d5437e2cbd60 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -48,7 +48,7 @@ options = bp.parse(ARGV, casts)
 
 Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 
-file_fasta = [options[:directory], "IDBA"].join(File::SEPARATOR) + ".fna"
+file_fasta = File.join(options[:directory], "IDBA") + ".fna"
 
 Fasta.open(file_fasta, mode="w") do |fasta_io|
   bp.each_record do |record|
@@ -57,7 +57,7 @@ Fasta.open(file_fasta, mode="w") do |fasta_io|
 end
 
 unless File.size(file_fasta) == 0
-  output = [options[:directory], "IDBA"].join(File::SEPARATOR)
+  output = File.join(options[:directory], "IDBA")
 
   commands = []
   commands << "nice -n 19"
@@ -82,7 +82,7 @@ unless File.size(file_fasta) == 0
     $stderr.puts "Command failed: #{command}"
   end
 
-  file_contig = [options[:directory], "IDBA"].join(File::SEPARATOR) + "-contig.fa"
+  file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
 
   Fasta.open(file_contig, mode="r") do |fasta_io|
     fasta_io.each do |entry|