--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mytools/splicesitescore/score5.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,102 @@
+use strict;
+
+
+my $inputfile = $ARGV[0];
+my $usemaxent = 1;
+
+my $modelpath = "/Users/xuebing/galaxy-dist/tools/mytools/splicesitescore/";
+my %me2x5 = &makescorematrix($modelpath.'me2x5');
+my %seq = &makesequencematrix($modelpath.'splicemodels/splice5sequences');
+
+my %bgd;
+$bgd{'A'} = 0.27;
+$bgd{'C'} = 0.23;
+$bgd{'G'} = 0.23;
+$bgd{'T'} = 0.27; 
+
+
+
+open (FILE,"<$inputfile") || die "can't open!\n";
+
+while(<FILE>) {
+    chomp;
+    if (/^\s*$/) { #discard blank lines;
+	next;
+    } 
+    elsif (/^>/) { #discard comment lines;
+        print $_."\t";
+	next;
+    }
+    elsif (/[NQWERYUIOPLKJHFDSZXVBM]/) {
+        next;
+    }
+    else {
+        $_ =~ s/\cM//g; #gets rid of carriage return
+	my $str = $_;
+	print $str."\t";
+	$str = uc($str);
+	if ($usemaxent) { 
+	 print sprintf("%.2f",&log2(&scoreconsensus($str)*$me2x5{$seq{&getrest($str)}}))."\n";
+	}
+    }
+}
+
+  
+sub makesequencematrix{
+    my $file = shift;
+    my %matrix;my $n=0;
+    open(SCOREF, $file) || die "Can't open $file!\n";
+    while(<SCOREF>) { 
+	chomp;
+	$_=~ s/\s//;
+	$matrix{$_} = $n;
+	$n++;
+    }
+    close(SCOREF);
+    return %matrix;
+}
+sub makescorematrix{
+    my $file = shift;
+    my %matrix;my $n=0;
+    open(SCOREF, $file) || die "Can't open $file!\n";
+    while(<SCOREF>) { 
+	chomp;
+	$_=~ s/\s//;
+	$matrix{$n} = $_;
+	$n++;
+    }
+    close(SCOREF);
+    return %matrix;
+}
+
+sub getrest{
+  my $seq = shift;
+  my @seqa = split(//,uc($seq));
+  return $seqa[0].$seqa[1].$seqa[2].$seqa[5].$seqa[6].$seqa[7].$seqa[8];
+}
+sub scoreconsensus{
+  my $seq = shift;
+  my @seqa = split(//,uc($seq));
+  my %bgd; 
+  $bgd{'A'} = 0.27; 
+  $bgd{'C'} = 0.23; 
+  $bgd{'G'} = 0.23; 
+  $bgd{'T'} = 0.27;  
+  my %cons1;
+  $cons1{'A'} = 0.004;
+  $cons1{'C'} = 0.0032;
+  $cons1{'G'} = 0.9896;
+  $cons1{'T'} = 0.0032;
+  my %cons2;
+  $cons2{'A'} = 0.0034; 
+  $cons2{'C'} = 0.0039; 
+  $cons2{'G'} = 0.0042; 
+  $cons2{'T'} = 0.9884;
+  my $addscore = $cons1{$seqa[3]}*$cons2{$seqa[4]}/($bgd{$seqa[3]}*$bgd{$seqa[4]}); 
+  return $addscore;
+}
+
+sub log2{
+      my ($val) = @_;
+    return log($val)/log(2);
+}