X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fassemble_seq_velvet;h=e2753ce91ad65023d47627bd1c372553075fb14e;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=d6106fc0f3fbe7c996282437d5c4c6d6d15ea628;hpb=9b109416b6dcbf422ad38d45d134c59f78221198;p=biopieces.git

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index d6106fc..e2753ce 100755
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -101,7 +101,7 @@ class Velvet
     count   = 0
     n50     = 0
 
-    Fasta.open(file, mode="r") do |fasta_io|
+    Fasta.open(file, "r") do |fasta_io|
       fasta_io.each do |entry|
         total   += entry.length
         lengths << entry.length
@@ -144,7 +144,7 @@ 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|
+  Fasta.open(file_fasta, "w") do |fasta_io|
     input.each_record do |record|
       if record[:SEQ_NAME] and record[:SEQ]
         seq = Seq.new_bp(record)
@@ -159,8 +159,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 		velvet.run_velvetg(options[:ins_length], options[:type].match("Paired"))
 		file_contigs = velvet.pick_best_assembly
 
-		Fasta.open(file_contigs, mode="r") do |fasta_io|
+    kmer = file_contigs.match(/_\d+/)
+
+		Fasta.open(file_contigs, "r") do |fasta_io|
 		  fasta_io.each do |entry|
+        entry.seq_name << "_kmer#{kmer}"
 			  output.puts entry.to_bp
 	    end
 		end