X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffind_genes;h=88dacf2ddee0c7ec899a13cf6f008a7b6380e61b;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=b365ab27a261d0cbf93d9659ce58009ca37ac26a;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index b365ab2..88dacf2 100755
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -37,30 +37,30 @@ casts = []
 casts << {:long=>'full',      :short=>'f', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
 casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
-
-tmpdir  = bp.mktmpdir
-infile  = "#{tmpdir}/in.fna"
-outfile = "#{tmpdir}/out.prodigal"
-
-Fasta.open(infile, mode="w") do |fasta_io|
-  bp.each_record do |record|
-    bp.puts record
-    fasta_io.puts record
+options = Biopieces.options_parse(ARGV, casts)
+
+tmpdir  = Biopieces.mktmpdir
+infile  = File.join(tmpdir, "in.fna")
+outfile = File.join(tmpdir, "out.prodigal")
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  Fasta.open(infile, "w") do |fasta_io|
+    input.each_record do |record|
+      output.puts record
+
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
+    end
   end
-end
 
-prodigal = Prodigal.new(infile, outfile, options)
-prodigal.run
+  prodigal = Prodigal.new(infile, outfile, options)
+  prodigal.run
 
-prodigal.each do |record|
-  record[:DEFINITION].match /seqhdr="([^"]+)/ do |m| 
-    record[:S_ID] = $1
+  prodigal.each do |record|
+    output.puts record
   end
-
-  bp.puts record
 end