removed debug message

[biopieces.git] / bp_bin / read_fasta

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index c0ab73f05642c5d585fc3a18e5fdfe92eeef59fe..e6494405f4ae7ebd844cebdebf67e495b036acfc 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -28,39 +28,41 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
 
 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, '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