X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffind_genes;h=88dacf2ddee0c7ec899a13cf6f008a7b6380e61b;hb=4868b7e6e097f3d0eb0d512b93c069437a80d153;hp=367b9766763d85fe21dc9b8a080c764e3b168926;hpb=be77de27ae5af645ff75447371cf9b0383273d00;p=biopieces.git

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index 367b976..88dacf2 100755
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -29,38 +29,38 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
-require 'fasta'
-require 'prodigal'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/prodigal'
 
 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 = Biopieces.options_parse(ARGV, casts)
 
-options = bp.parse(ARGV, casts)
+tmpdir  = Biopieces.mktmpdir
+infile  = File.join(tmpdir, "in.fna")
+outfile = File.join(tmpdir, "out.prodigal")
 
-tmpdir  = bp.mktmpdir
-infile  = "#{tmpdir}/in.fna"
-outfile = "#{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
 
-Fasta.open(infile, mode="w") do |fasta_io|
-  bp.each_record do |record|
-    bp.puts 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
-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