# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Assemble sequences in the stream using IDBA-UD.
+# Assemble sequences in the stream using idba hybrid.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
-file_fasta = File.join(options[:directory], "IDBA-UD") + ".fna"
+file_fasta = File.join(options[:directory], "IDBA-HYBRID") + ".fna"
count = 0
end
unless File.size(file_fasta) == 0
- prefix = File.join(options[:directory], "IDBA-UD")
+ prefix = File.join(options[:directory], "IDBA-HYBRID")
commands = []
- commands << "nice -n 19"
- commands << "idba_ud"
+ commands << "idba_hybrid"
commands << "--read #{file_fasta}"
commands << "--out #{prefix}"
commands << "--mink #{options[:kmer_min]}"
system(command)
raise "Command failed: #{command}" unless $?.success?
- file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa")
+ file_contig = File.join(options[:directory], "IDBA-HYBRID", "contig.fa")
Fasta.open(file_contig, "r") do |fasta_io|
fasta_io.each do |entry|