refactoring of revcomp in seq.rb

[biopieces.git] / bp_bin / pcr_seq

diff --git a/bp_bin/pcr_seq b/bp_bin/pcr_seq
index f54577373e75f7f32f24752c3a54ff31eaedafa8..57eb447b3684d51f7346bb6a111c2c386937b776 100755 (executable)
--- a/bp_bin/pcr_seq
+++ b/bp_bin/pcr_seq
@@ -51,6 +51,7 @@ class Pcr
 
       command =  "scan_for_matches"
       # command << " -c"
+      command << " -o 1"
       command << " #{pat_file}"
       command << " < #{@infile}"
       command << " > #{outfile}"
@@ -145,21 +146,32 @@ class Pattern
     seq      = Seq.new
     seq.seq  = primer
     seq.type = 'dna'
-    seq.revcomp
+    seq.reverse!.complement!
 
     descriptor ? seq.seq + descriptor : seq.seq
   end
 end
 
 casts = []
-casts << {:long=>'forward',  :short=>'f', :type=>'string', :mandatory=>true, :default=>nil,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'reverse',  :short=>'r', :type=>'string', :mandatory=>true, :default=>nil,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'max_dist', :short=>'m', :type=>'uint',   :mandatory=>true, :default=>5000, :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'forward',    :short=>'f', :type=>'string', :mandatory=>false, :default=>nil,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'forward_rc', :short=>'F', :type=>'string', :mandatory=>false, :default=>nil,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse',    :short=>'r', :type=>'string', :mandatory=>false, :default=>nil,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse_rc', :short=>'R', :type=>'string', :mandatory=>false, :default=>nil,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'max_dist',   :short=>'m', :type=>'uint',   :mandatory=>true, :default=>5000, :allowed=>nil, :disallowed=>"0"}
 
 options = Biopieces.options_parse(ARGV, casts)
 tmpdir  = Biopieces.mktmpdir
 infile  = File.join(tmpdir, "in.fna")
 
+if options[:forward_rc]
+  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').reverse.complement.seq
+end
+
+raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   Fasta.open(infile, mode="w") do |ios|
     input.each_record do |record|
@@ -183,8 +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]