X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffind_genes;h=15e7f5703a74703a30f193cfcb5495beaa80d86f;hb=4926ddf7ba9dd7273dfcdedad8141833330f5d67;hp=f0d64c8365300b3c970dd43fd6f6f7c1ed67f9e1;hpb=49160fe9cb5472914fc4596a27605898974212ed;p=biopieces.git

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index f0d64c8..15e7f57 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=>'full', :short=>'p', :type=>'procedure', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
+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, mode="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