--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maxent_score3.pl	Sun Apr 01 08:24:20 2012 -0400
@@ -0,0 +1,125 @@
+use strict;
+
+
+my $inputfile = $ARGV[0];
+my $usemaxent = 1;
+
+my $modelpath = "/home/sharp-galaxy.orig/tools/maxentscan/splicemodels/";
+my @metables = &makemaxentscores($modelpath);
+
+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)*&maxentscore(&getrest($str),\@metables)))."\n";
+	}
+    }
+}
+
+sub hashseq{
+    #returns hash of sequence in base 4
+    # &hashseq('CAGAAGT') returns 4619
+    my $seq = shift;
+    $seq = uc($seq);
+    $seq =~ tr/ACGT/0123/;
+    my @seqa = split(//,$seq);
+    my $sum = 0;
+    my $len = length($seq);
+    my @four = (1,4,16,64,256,1024,4096,16384);
+    my $i=0;
+    while ($i<$len) {
+        $sum+= $seqa[$i] * $four[$len - $i -1] ;
+	$i++;
+    }
+    return $sum;
+}
+
+sub makemaxentscores{
+    my $dir = shift;
+    my @list = ('me2x3acc1','me2x3acc2','me2x3acc3','me2x3acc4',
+		'me2x3acc5','me2x3acc6','me2x3acc7','me2x3acc8','me2x3acc9');
+    my @metables;
+    my $num = 0 ;
+    foreach my $file (@list) {
+	my $n = 0;
+	open (SCOREF,"<".$dir.$file) || die "Can't open $file!\n";
+	while(<SCOREF>) {
+	    chomp;
+	    $_=~ s/\s//;
+	    $metables[$num]{$n} = $_;
+	    $n++;
+	}
+	close(SCOREF);
+	#print STDERR $file."\t".$num."\t".$n."\n";
+	$num++;
+    }
+    return @metables;
+}
+
+sub maxentscore{
+    my $seq = shift;
+    my $table_ref = shift;
+    my @metables = @$table_ref;
+    my @sc;
+    $sc[0] = $metables[0]{&hashseq(substr($seq,0,7))};
+    $sc[1] = $metables[1]{&hashseq(substr($seq,7,7))};
+    $sc[2] = $metables[2]{&hashseq(substr($seq,14,7))};
+    $sc[3] = $metables[3]{&hashseq(substr($seq,4,7))};
+    $sc[4] = $metables[4]{&hashseq(substr($seq,11,7))};
+    $sc[5] = $metables[5]{&hashseq(substr($seq,4,3))};
+    $sc[6] = $metables[6]{&hashseq(substr($seq,7,4))};
+    $sc[7] = $metables[7]{&hashseq(substr($seq,11,3))};
+    $sc[8] = $metables[8]{&hashseq(substr($seq,14,4))};
+    my $finalscore = $sc[0] * $sc[1] * $sc[2] * $sc[3] * $sc[4] / ($sc[5] * $sc[6] * $sc[7] * $sc[8]);
+    return $finalscore;
+}    
+    
+
+
+sub getrest{
+  my $seq = shift;
+  my $seq_noconsensus = substr($seq,0,18).substr($seq,20,3);
+  return $seq_noconsensus;
+}
+
+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'} = 0.9903;
+  $cons1{'C'} = 0.0032;
+  $cons1{'G'} = 0.0034;
+  $cons1{'T'} = 0.0030;
+  my %cons2;
+  $cons2{'A'} = 0.0027; 
+  $cons2{'C'} = 0.0037; 
+  $cons2{'G'} = 0.9905; 
+  $cons2{'T'} = 0.0030;
+  my $addscore = $cons1{$seqa[18]} * $cons2{$seqa[19]}/ ($bgd{$seqa[18]} * $bgd{$seqa[19]}); 
+  return $addscore;
+}
+sub log2{
+      my ($val) = @_;
+    return log($val)/log(2);
+}