From d90521fe9b7bf51683eb4722bd223e143a53270b Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 13 Oct 2011 12:11:20 +0000
Subject: [PATCH] fixed assemblers

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1563 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/analyze_assembly    |  4 +++-
 bp_bin/assemble_seq_idba   | 20 ++++++++++++--------
 bp_bin/assemble_seq_ray    |  6 +++++-
 bp_bin/assemble_seq_velvet | 11 +++++++----
 4 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
index 7fe7bd6..3b9748d 100755
--- a/bp_bin/analyze_assembly
+++ b/bp_bin/analyze_assembly
@@ -54,12 +54,14 @@ Fasta.open(infile, mode="w") do |fasta_output|
   Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     input.each_record do |record|
       if record.has_key? :SEQ
+        seq = Seq.new_bp(record)
+
         total   += record[:SEQ].length
         lengths << record[:SEQ].length
       end
 
       output.puts record unless options[:no_stream]
-      fasta_output.puts record
+      fasta_output.puts seq.to_fasta
     end
   end
 end
diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 1f392e9..2b65543 100755
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -53,17 +53,21 @@ count = 0
 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|
-      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"
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
 
-          count += 1
+        if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
+          if seq.seq_name =~ /1$/
+            seq.seq_name = "read#{count}/1"
+          else
+            seq.seq_name = "read#{count}/2"
+
+            count += 1
+          end
         end
-      end
 
-			fasta_io.puts record
+        fasta_io.puts seq.to_fasta
+      end
 		end
 	end
 
diff --git a/bp_bin/assemble_seq_ray b/bp_bin/assemble_seq_ray
index 441fb50..fbef82a 100755
--- a/bp_bin/assemble_seq_ray
+++ b/bp_bin/assemble_seq_ray
@@ -141,7 +141,11 @@ file_fasta = File.join(options[:directory], "sequence_in.fasta")
 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
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+
+			  fasta_io.puts seq.to_fasta
+      end
 		end
 	end
 
diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 71fc5c1..98c0ba4 100755
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -161,10 +161,13 @@ Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 file_fasta = File.join(options[:directory], "sequence_in.fna")
 
 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
+  Fasta.open(file_fasta, mode="w") do |fasta_io|
+    input.each_record do |record|
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
+    end
 	end
 
 	unless File.size(file_fasta) == 0
-- 
2.39.2