polished assemble_seq_idba

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1361 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 861e0380ee6410ab731c51e211221ac776ebb2bf..812fe5fb81cd0975b195aa317f0a0f346bd35b55 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -30,9 +30,6 @@
 
 require 'biopieces'
 require 'fasta'
-require 'pp'
-
-ok_methods = "ublast,usearch,uclust,usearch_uclust"
 
 casts = []
 casts << {:long=>'name',        :short=>'n', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
@@ -44,7 +41,6 @@ casts << {:long=>'count_min',   :short=>'c', :type=>'uint',   :mandatory=>false,
 casts << {:long=>'cover',       :short=>'C', :type=>'uint',   :mandatory=>false, :default=>0,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'pairs_min',   :short=>'p', :type=>'uint',   :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'prefix_len',  :short=>'P', :type=>'uint',   :mandatory=>false, :default=>3,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream',   :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 bp = Biopieces.new
 
@@ -60,25 +56,35 @@ Fasta.open(file_fasta, mode="w") do |fasta_io|
   end
 end
 
-output = [options[:directory], options[:name] ].join(File::SEPARATOR)
-
-commands = []
-commands << "nice -n 19"
-commands << "idba"
-commands << "--read #{file_fasta}"
-commands << "--output #{output}"
-commands << "--scaffold" if options[:scaffold]
-commands << "--mink #{options[:k_value_min]}"
-commands << "--maxk #{options[:k_value_max]}"
-commands << "--minCount #{options[:count_min]}"
-commands << "--cover #{options[:cover]}"
-commands << "--minPairs #{options[:pairs_min]}"
-commands << "--prefixLength #{options[:prefix_len]}"
-commands << "> /dev/null 2>&1" unless options[:verbose]
-
-command = commands.join(" ")
-system(command)
-raise "Command failed: #{command}" unless $?.success?
+unless File.size(file_fasta) == 0
+  output = [options[:directory], options[:name] ].join(File::SEPARATOR)
+
+  commands = []
+  commands << "nice -n 19"
+  commands << "idba"
+  commands << "--read #{file_fasta}"
+  commands << "--output #{output}"
+  commands << "--scaffold" if options[:scaffold]
+  commands << "--mink #{options[:k_value_min]}"
+  commands << "--maxk #{options[:k_value_max]}"
+  commands << "--minCount #{options[:count_min]}"
+  commands << "--cover #{options[:cover]}"
+  commands << "--minPairs #{options[:pairs_min]}"
+  commands << "--prefixLength #{options[:prefix_len]}"
+  commands << "> /dev/null 2>&1" unless options[:verbose]
+
+  command = commands.join(" ")
+  system(command)
+  raise "Command failed: #{command}" unless $?.success?
+
+  file_contig = [options[:directory], options[:name] ].join(File::SEPARATOR) + "-contig.fa"
+
+  Fasta.open(file_contig, mode="r") do |fasta_io|
+    fasta_io.each do |entry|
+      bp.puts entry.to_bp
+    end
+  end
+end
 
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