clearning up kmer_stats and kmer_freq

[biopieces.git] / bp_bin / assemble_seq_velvet

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 7569811eba6537c4af52e5c21fb70207375bb057..98c0ba4486a23d47b6969cd9d56d2a4e1902f24b 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -148,7 +148,7 @@ casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>true,
 casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint',   :mandatory=>true,  :default=>31,          :allowed=>nil,   :disallowed=>nil}
 casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list',   :mandatory=>true,  :default=>cov_cutoffs, :allowed=>nil,   :disallowed=>nil}
 casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',      :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'clean',      :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,         :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)
 
@@ -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