diff MISA/p3_in.pl @ 0:3006582bfc76

Uploaded V1.0 MISA tools and helper scripts

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MISA/p3_in.pl	Wed Sep 14 23:57:57 2011 -0400
@@ -0,0 +1,34 @@
+#!/usr/bin/perl -w
+# Author: Thomas Thiel
+# Program name: primer3_in.pl
+# Description: creates a PRIMER3 input file based on SSR search results
+
+open (IN,"<$ARGV[0]") || die ("\nError: Couldn't open misa.pl results file (*.misa) !\n\n");
+
+#my $filename = $ARGV[0];
+#$filename =~ s/\.misa//;
+open (SRC,"<$ARGV[1]") || die ("\nError: Couldn't open source file containing original FASTA sequences !\n\n");
+open (OUT,">$ARGV[2]");
+
+undef $/;
+$in = <IN>;
+study $in;
+
+$/= ">";
+
+#my $count;
+while (<SRC>)
+  {
+  next unless (my ($id,$seq) = /(.*?)\n(.*)/s);
+  $seq =~ s/[\d\s>]//g;#remove digits, spaces, line breaks,...
+  while ($in =~ /$id\t(\d+)\t\S+\t\S+\t(\d+)\t(\d+)/g)
+    {
+    my ($ssr_nr,$size,$start) = ($1,$2,$3);
+    #$count++;
+    print OUT "PRIMER_SEQUENCE_ID=$id"."_$ssr_nr\nSEQUENCE=$seq\n";
+    print OUT "PRIMER_PRODUCT_SIZE_RANGE=100-280\n";
+    print OUT "TARGET=",$start-3,",",$size+6,"\n";
+    print OUT "PRIMER_MAX_END_STABILITY=250\n=\n"
+    };
+  };
+#print "\n$count records created.\n";