X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fanalyze_assembly;h=614a9e54d8e85bc00e84e2a6deab96049c0ddb5d;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=bcc727ca9a97f47fee777a018abea8b1e359623a;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
index bcc727c..614a9e5 100755
--- a/bp_bin/analyze_assembly
+++ b/bp_bin/analyze_assembly
@@ -40,27 +40,29 @@ casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true,  :
 casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
 casts << {:long=>'data_out',  :short=>'o', :type=>'file',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
 
 options[:full] = true;
 
 total   = 0
 lengths = []
-tmpdir  = bp.mktmpdir
-infile  = "#{tmpdir}/in.fna"
-outfile = "#{tmpdir}/out.prodigal"
-
-Fasta.open(infile, mode="w") do |fasta_io|
-  bp.each_record do |record|
-    if record.has_key? :SEQ
-      total   += record[:SEQ].length
-      lengths << record[:SEQ].length
+tmpdir  = Biopieces.mktmpdir
+infile  = File.join(tmpdir, "in.fna")
+outfile = File.join(tmpdir, "out.prodigal")
+
+Fasta.open(infile, "w") do |fasta_output|
+  Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+    input.each_record do |record|
+      if record[:SEQ]
+        seq = Seq.new_bp(record)
+
+        total   += record[:SEQ].length
+        lengths << record[:SEQ].length
+      end
+
+      output.puts record unless options[:no_stream]
+      fasta_output.puts seq.to_fasta
     end
-
-    bp.puts record unless options[:no_stream]
-    fasta_io.puts record
   end
 end
 
@@ -82,8 +84,6 @@ lengths.sort.reverse.each do |length|
   end
 end
 
-bp.out = Stream.write(options[:data_out]) if options[:data_out]
-
 new_record = {}
 new_record[:N50]        = n50
 new_record[:MAX]        = lengths.max
@@ -93,7 +93,10 @@ new_record[:TOTAL]      = total
 new_record[:COUNT]      = lengths.size
 new_record[:GENE_COV]   = gene_cov if options[:gene_cov]
 
-bp.puts new_record
+Biopieces.open(nil, options[:data_out]) do |input, output|
+  output.puts new_record
+end
+
 
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