refactoring of ruby code s/has_key?/[]/

[biopieces.git] / bp_bin / blast_seq_pair

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index 0bf097a32f93855864b483d36d30a69b68a111ee..1963eafc4b128d94579d6d02e86cddf14964962c 100755 (executable)
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -143,7 +143,7 @@ ok_programs = "blastn,blastp,tblastn,blastx,tblastx"
 
 casts = []
 casts << {:long=>'program',   :short=>'p', :type=>'string', :mandatory=>false, :default=>nil,  :allowed=>ok_programs, :disallowed=>nil}
-casts << {:long=>'e_val',     :short=>'e', :type=>'float',  :mandatory=>false, :default=>10,   :allowed=>nil,         :disallowed=>nil}
+casts << {:long=>'e_val',     :short=>'e', :type=>'float',  :mandatory=>false, :default=>10.0, :allowed=>nil,         :disallowed=>nil}
 casts << {:long=>'filter',    :short=>'f', :type=>'string', :mandatory=>false, :default=>'no', :allowed=>'yes,no',    :disallowed=>nil}
 casts << {:long=>'megablast', :short=>'m', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
 casts << {:long=>'no_gaps',   :short=>'G', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
@@ -164,19 +164,22 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     output.puts record
 
-    if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+    if record[:SEQ_NAME] and record[:SEQ]
+      seq = Seq.new_bp(record)
+
       unless got1
         Fasta.open(infile1, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got1  = true
         type1 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
+        next
       end
 
       unless got2
         Fasta.open(infile2, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got2  = true