updateing to idba hybrid

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2279 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 87b81a2675769dfa0dc411a48bea9d4303df3383..fcf13f866790cac67314f340ccad69a10f54df7d 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Assemble sequences in the stream using IDBA-UD.
+# Assemble sequences in the stream using idba hybrid.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -38,14 +38,14 @@ casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :d
 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
 
@@ -61,11 +61,10 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
        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]}"
@@ -81,7 +80,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
          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|