fixed asseble_seq_velvet

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1422 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 08629852c921b42ed75011879489e6a771520a9e..7569811eba6537c4af52e5c21fb70207375bb057 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -150,9 +150,7 @@ casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list',   :mandatory=>true,
 casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',      :allowed=>nil,   :disallowed=>nil}
 casts << {:long=>'clean',      :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,         :allowed=>nil,   :disallowed=>nil}
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
 
 raise ArgumentError, "kmer_min #{options[:kmer_min]} must be uneven." if options[:kmer_min].even?
 raise ArgumentError, "kmer_max #{options[:kmer_max]} must be uneven." if options[:kmer_max].even?
@@ -162,23 +160,25 @@ Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 
 file_fasta = File.join(options[:directory], "sequence_in.fna")
 
-Fasta.open(file_fasta, mode="w") do |fasta_io|
-  bp.each_record do |record|
-    fasta_io.puts record
-  end
-end
-
-unless File.size(file_fasta) == 0
-  velvet = Velvet.new(options[:directory], file_fasta, options[:verbose])
-  velvet.run_velveth(options[:kmer_min], options[:kmer_max], options[:type])
-  velvet.run_velvetg(options[:cov_cutoff], options[:exp_cov])
-  file_contigs = velvet.pick_best_assembly
-
-  Fasta.open(file_contigs, mode="r") do |fasta_io|
-    fasta_io.each do |entry|
-      bp.puts entry.to_bp
-    end
-  end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+       Fasta.open(file_fasta, mode="w") do |fasta_io|
+               input.each_record do |record|
+                       fasta_io.puts record
+               end
+       end
+
+       unless File.size(file_fasta) == 0
+               velvet = Velvet.new(options[:directory], file_fasta, options[:verbose])
+               velvet.run_velveth(options[:kmer_min], options[:kmer_max], options[:type])
+               velvet.run_velvetg(options[:cov_cutoff], options[:exp_cov])
+               file_contigs = velvet.pick_best_assembly
+
+               Fasta.open(file_contigs, mode="r") do |fasta_io|
+                       fasta_io.each do |entry|
+                               output.puts entry.to_bp
+                       end
+               end
+       end
 end
 
 FileUtils.remove_entry_secure file_fasta