added missing files

[biopieces.git] / bp_bin / read_fasta

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 9b77008554c1dece44c0fcb257d7c9375bcf87b4..8bc5874f55dc0a6399e78c6a29167af9fdb773c1 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -35,32 +35,34 @@ casts = []
 casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
 
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
 
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
-  bp.puts record
-end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  unless options[:data_in] and options[:data_in].first == '-'
+    input.each_record do |record|
+      output.puts record
+    end
+  end
 
-num  = 0
-last = false
+  num  = 0
+  last = false
 
-if options.has_key? :data_in
-  options[:data_in].each do |file|
-    Fasta.open(file, mode='r') do |fasta|
-      fasta.each do |entry|
-        bp.puts entry.to_bp
-        num += 1
+  if options[:data_in]
+    options[:data_in].each do |file|
+      Fasta.open(file, mode='r') do |fasta|
+        fasta.each do |entry|
+          output.puts entry.to_bp
+          num += 1
 
-        if options.has_key? :num and options[:num] == num
-          last = true
-          break
+          if options[:num] and options[:num] == num
+            last = true
+            break
+          end
         end
       end
-    end
 
-    break if last
+      break if last
+    end
   end
 end