From 768fdc708b1fa7a5241b0c46116e0c231fefb666 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 24 May 2011 11:39:39 +0000
Subject: [PATCH] fixed asseble_seq_idba

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1421 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/assemble_seq_idba | 84 ++++++++++++++++++++--------------------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index ef35973..a8b6c25 100755
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -42,53 +42,53 @@ casts << {:long=>'pairs_min',  :short=>'p', :type=>'uint',   :mandatory=>false,
 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}
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
 
 Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 
 file_fasta = File.join(options[:directory], "IDBA") + ".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
-  output = File.join(options[:directory], "IDBA")
-
-  commands = []
-  commands << "nice -n 19"
-  commands << "idba"
-  commands << "--read #{file_fasta}"
-  commands << "--output #{output}"
-  commands << "--scaffold" if options[:scaffold]
-  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 << "> /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
-
-  file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
-
-  Fasta.open(file_contig, 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
+		prefix = File.join(options[:directory], "IDBA")
+
+		commands = []
+		commands << "nice -n 19"
+		commands << "idba"
+		commands << "--read #{file_fasta}"
+		commands << "--output #{prefix}"
+		commands << "--scaffold" if options[:scaffold]
+		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 << "> /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
+
+		file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
+
+		Fasta.open(file_contig, 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
-- 
2.39.2