X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fpcr_seq;h=f6c874e7e9555e021c83f5213f6277e2f8f591ff;hb=5a9b7c80e4e4428e404575ed3c0290cde15a7402;hp=8700276e16287559ed9fe37f1d33b8c26c382e7a;hpb=5ced0e7864e9645e56c6c618da1f04e0a4d667fc;p=biopieces.git

diff --git a/bp_bin/pcr_seq b/bp_bin/pcr_seq
index 8700276..f6c874e 100755
--- a/bp_bin/pcr_seq
+++ b/bp_bin/pcr_seq
@@ -146,7 +146,7 @@ class Pattern
     seq      = Seq.new
     seq.seq  = primer
     seq.type = 'dna'
-    seq.revcomp
+    seq.reverse!.complement!
 
     descriptor ? seq.seq + descriptor : seq.seq
   end
@@ -164,11 +164,11 @@ tmpdir  = Biopieces.mktmpdir
 infile  = File.join(tmpdir, "in.fna")
 
 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]
@@ -177,7 +177,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     input.each_record do |record|
       output.puts record
 
-      if record.has_key? :SEQ
+      if record[:SEQ]
         entry = Seq.new_bp(record)
         ios.puts entry.to_fasta
       end
@@ -195,8 +195,8 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         record[:TYPE]     = File.basename(outfile).sub(".fna", "").upcase
         record[:SEQ_NAME].match(/(.+):\[(\d+),(\d+)\]$/)
         record[:SEQ_NAME] = $1
-        record[:PCR_BEG]  = $2
-        record[:PCR_END]  = $3
+        record[:PCR_BEG]  = $2.to_i
+        record[:PCR_END]  = $3.to_i
 
         if record[:PCR_BEG] > record[:PCR_END]
           record[:PCR_BEG], record[:PCR_END] = record[:PCR_END], record[:PCR_BEG]