X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fassemble_seq_idba;h=87b81a2675769dfa0dc411a48bea9d4303df3383;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=e6a1290e7431c3293f7551d880fcbf5edd40a910;hpb=c2881d9159862295233b4895deb8bbebba0fbe99;p=biopieces.git

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index e6a1290..87b81a2 100755
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 
-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2012 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Assemble sequences in the stream using IDBA.
+# Assemble sequences in the stream using IDBA-UD.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -33,73 +33,57 @@ require 'maasha/fasta'
 
 casts = []
 casts << {:long=>'directory',  :short=>'d', :type=>'dir',  :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'scaffold',   :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>25,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :default=>50,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>20,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :default=>100, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'count_min',  :short=>'c', :type=>'uint', :mandatory=>false, :default=>2,   :allowed=>nil, :disallowed=>nil}
-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=>'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=>'clean',      :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus',       :short=>'C', :type=>'uint', :mandatory=>false, :default=>0,   :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") + ".fna"
+file_fasta = File.join(options[:directory], "IDBA-UD") + ".fna"
 
 count = 0
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-	Fasta.open(file_fasta, mode="w") do |fasta_io|
+	Fasta.open(file_fasta, "w") do |fasta_io|
 		input.each_record do |record|
-      if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
-        if record[:SEQ_NAME] =~ /1$/
-          record[:SEQ_NAME] = "read#{count}/1"
-        else
-          record[:SEQ_NAME] = "read#{count}/2"
-
-          count += 1
-        end
-      end
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
 
-			fasta_io.puts record
+        fasta_io.puts seq.to_fasta
+      end
 		end
 	end
 
 	unless File.size(file_fasta) == 0
-		prefix = File.join(options[:directory], "IDBA")
+		prefix = File.join(options[:directory], "IDBA-UD")
 
 		commands = []
 		commands << "nice -n 19"
-		commands << "idba"
+		commands << "idba_ud"
 		commands << "--read #{file_fasta}"
-		commands << "--output #{prefix}"
-		commands << "--scaffold" if options[:scaffold]
+		commands << "--out #{prefix}"
 		commands << "--mink #{options[:kmer_min]}"
 		commands << "--maxk #{options[:kmer_max]}"
-		commands << "--minCount #{options[:count_min]}"
-		commands << "--cover #{options[:cover]}"
-		commands << "--minPairs #{options[:pairs_min]}"
-		commands << "--prefixLength #{options[:prefix_len]}"
+		commands << "--min_count #{options[:count_min]}"
+		commands << "--min_pairs #{options[:pairs_min]}"
+		commands << "--prefix #{options[:prefix_len]}"
+		commands << "--num_threads #{options[:cpus]}"
 		commands << "> /dev/null 2>&1" unless options[:verbose]
 
 		command = commands.join(" ")
 
-		begin
-			system(command)
-			raise "Command failed: #{command}" unless $?.success?
-		rescue
-			$stderr.puts "Command failed: #{command}"
-		end
+	  system(command)
+	  raise "Command failed: #{command}" unless $?.success?
 
-    if options[:scaffold]
-		  file_contig = File.join(options[:directory], "IDBA") + "-contig-mate.fa"
-    else
-		  file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
-    end
+    file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa")
 
-		Fasta.open(file_contig, mode="r") do |fasta_io|
+		Fasta.open(file_contig, "r") do |fasta_io|
 			fasta_io.each do |entry|
 				output.puts entry.to_bp
 			end