diff MISA/p3_out.pl @ 0:3006582bfc76

Uploaded V1.0 MISA tools and helper scripts

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MISA/p3_out.pl	Wed Sep 14 23:57:57 2011 -0400
@@ -0,0 +1,76 @@
+#!/usr/bin/perl -w
+# Author: Thomas Thiel
+# Program name: prim_output.pl
+# Description: converts the Primer3 output into an table
+
+open (SRC,"<$ARGV[0]") || die ("\nError: Couldn't open Primer3 results file (*.p3out) !\n\n");
+my $filename = $ARGV[0];
+$filename =~ s/\.p3out//;
+open (IN,"<$ARGV[1]") || die ("\nError: Couldn't open source file containing MISA (*.misa) results !\n\n");
+open (OUT,">$ARGV[2]") || die ("nError: Couldn't create file !\n\n");
+
+my ($seq_names_failed,$count_failed,$count);
+print OUT "ID\tSSR nr.\tSSR type\tSSR\tsize\tstart\tend\t";
+print OUT "FORWARD PRIMER1 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER1 (5'-3')\tTm(°C)\tsize\tPRODUCT1 size (bp)\tstart (bp)\tend (bp)\t";
+print OUT "FORWARD PRIMER2 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER2 (5'-3')\tTm(°C)\tsize\tPRODUCT2 size (bp)\tstart (bp)\tend (bp)\t";
+print OUT "FORWARD PRIMER3 (5'-3')\tTm(°C)\tsize\tREVERSE PRIMER3 (5'-3')\tTm(°C)\tsize\tPRODUCT3 size (bp)\tstart (bp)\tend (bp)\n";
+
+undef $/;
+my $in = <IN>;
+study $in;
+
+$/ = "=\n";
+
+while (<SRC>)
+  {
+  my ($id,$ssr_nr) = (/PRIMER_SEQUENCE_ID=(\S+)_(\d+)/);
+  
+  $in =~ /($id\t$ssr_nr\t.*)\n/;
+  my $misa = $1;
+  
+  /PRIMER_LEFT_SEQUENCE=(.*)/ || do {$count_failed++;print OUT "$misa\n"; next};
+  my $info = "$1\t";
+  
+  /PRIMER_LEFT_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT=\d+,(\d+)/; $info .= "$1\t";
+  
+  /PRIMER_RIGHT_SEQUENCE=(.*)/;  $info .= "$1\t";
+  /PRIMER_RIGHT_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_RIGHT=\d+,(\d+)/; $info .= "$1\t";
+  
+  /PRIMER_PRODUCT_SIZE=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT=(\d+),\d+/; $info .= "$1\t";
+  /PRIMER_RIGHT=(\d+),\d+/; $info .= "$1\t";
+  
+  
+  /PRIMER_LEFT_1_SEQUENCE=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_1_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_1=\d+,(\d+)/; $info .= "$1\t";
+    
+  /PRIMER_RIGHT_1_SEQUENCE=(.*)/;  $info .= "$1\t";
+  /PRIMER_RIGHT_1_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_RIGHT_1=\d+,(\d+)/; $info .= "$1\t";
+  
+  /PRIMER_PRODUCT_SIZE_1=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_1=(\d+),\d+/; $info .= "$1\t";
+  /PRIMER_RIGHT_1=(\d+),\d+/; $info .= "$1\t";
+  
+  
+  /PRIMER_LEFT_2_SEQUENCE=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_2_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_2=\d+,(\d+)/; $info .= "$1\t";
+    
+  /PRIMER_RIGHT_2_SEQUENCE=(.*)/;  $info .= "$1\t";
+  /PRIMER_RIGHT_2_TM=(.*)/; $info .= "$1\t";
+  /PRIMER_RIGHT_2=\d+,(\d+)/; $info .= "$1\t";
+  
+  /PRIMER_PRODUCT_SIZE_2=(.*)/; $info .= "$1\t";
+  /PRIMER_LEFT_2=(\d+),\d+/; $info .= "$1\t";
+  /PRIMER_RIGHT_2=(\d+),\d+/; $info .= "$1";
+  
+  $count++;
+  print OUT "$misa\t$info\n"
+  };
+
+#print "\nPrimer modelling was successful for $count sequences.\n";
+#print "Primer modelling failed for $count_failed sequences.\n";