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|
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"
$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|
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)
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
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|