refactoring of ruby code converting sequences types to symbols

[biopieces.git] / bp_bin / find_adaptor

diff --git a/bp_bin/find_adaptor b/bp_bin/find_adaptor
index 0534572bd4ff08669f934a57d1d1bfc9a64d9486..f2f593d1ce90f11087b04ca9d2abc8a58a40b264 100755 (executable)
--- a/bp_bin/find_adaptor
+++ b/bp_bin/find_adaptor
@@ -53,11 +53,11 @@ casts << {:long=>'deletions',   :short=>'d', :type=>'uint',   :mandatory=>false,
 options = Biopieces.options_parse(ARGV, casts)
 
 if options[:forward_rc]
-  options[:forward] = Seq.new("test", options[:forward_rc], 'dna').revcomp.seq
+  options[:forward] = Seq.new("test", options[:forward_rc], :dna).reverse.complement.seq
 end
 
 if options[:reverse_rc]
-  options[:reverse] = Seq.new("test", options[:reverse_rc], 'dna').revcomp.seq
+  options[:reverse] = Seq.new("test", options[:reverse_rc], :dna).reverse.complement.seq
 end
 
 raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
@@ -88,10 +88,10 @@ end
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each do |record|
-    if record[:SEQ] and record[:SEQ].length > 0
+    if record[:SEQ]
       entry = Seq.new_bp(record)
 
-      if options[:forward]
+      if options[:forward] and record[:SEQ].length >= options[:forward].length
         if m = entry.patmatch(options[:forward], 0, fmis, fins, fdel)
           record[:ADAPTOR_POS_LEFT] = m.pos
           record[:ADAPTOR_LEN_LEFT] = m.length
@@ -120,7 +120,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         end
       end
 
-      if options[:reverse]
+      if options[:reverse] and record[:SEQ].length >= options[:reverse].length
         if m = entry.patmatch(options[:reverse], 0, rmis, rins, rdel)
           record[:ADAPTOR_POS_RIGHT] = m.pos
           record[:ADAPTOR_LEN_RIGHT] = m.length