refactoring of assemble_pairs

[biopieces.git] / bp_bin / read_fasta

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 82a69a2424d9daa4f849b812edb6c8dee477386e..e6494405f4ae7ebd844cebdebf67e495b036acfc 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -38,7 +38,7 @@ casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :de
 options = Biopieces.options_parse(ARGV, casts)
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  unless options[:data_in].first == '-'
+  unless options[:data_in] and options[:data_in].first == '-'
     input.each_record do |record|
       output.puts record
     end
@@ -47,14 +47,14 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   num  = 0
   last = false
 
-  if options.has_key? :data_in
+  if options[:data_in]
     options[:data_in].each do |file|
-      Fasta.open(file, mode='r') do |fasta|
+      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
+          if options[:num] and options[:num] == num
             last = true
             break
           end