From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 18 May 2011 15:18:59 +0000 (+0000)
Subject: fixed paths in assemble_seq_idba + velvet
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e32bb0ffd1e353ebf1163007f31b7d15cdff3c97;p=biopieces.git

fixed paths in assemble_seq_idba + velvet

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1409 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index da2f4da..ef35973 100755
--- 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|
diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index c3e25f3..0862985 100755
--- 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|