--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_primersearch.pl	Thu Jun 14 19:29:26 2012 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/perl
+#parse_primersearch.pl
+#reformat EMBOSS primersearch output into columnar Galaxy interval format 
+
+#Copyright 2012 John McCallum 
+#New Zealand Institute for Plant and Food Research
+#This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+open (IN, "<$ARGV[0]");
+open (OUT, ">$ARGV[1]");
+
+#print OUT  "primerset_id","\t","sequence_id","\t","hit_start","\","mismatches","\t","amplimer_size",\n";
+
+
+
+while (<IN>) {
+         /^Primer name (\S+)/  && ($name = $1);  # get primer set name
+         # Modified to cope with unnamed sequence input 28/7/05
+        /Sequence: (\S+)/ && print OUT  $name,"\t",$1;
+        /Sequence:(\s{4,})/ && print OUT $name,"\t","unnamed_seq";
+        /hits forward strand at (\d+) with (\d) mismatches/ && ($start = $1) &&  print OUT  "\t",$2,"\t",$start,;
+        /Amplimer length: (\S+)/ && ($amp_length = $1) &&  print OUT "\t",$start + $amp_length,"\t",$1,"\n";
+        }
+
+close( IN );
+close( OUT );