# HG changeset patch
# User xuebing
# Date 1333282485 14400
# Node ID ec97befe722b32092f4b7e94492b9e13435f078b
# Parent  3fd430270c0c855f4ec49016c4afd35007f29530
Uploaded

diff -r 3fd430270c0c -r ec97befe722b splicesite.xml
--- a/splicesite.xml	Sun Apr 01 01:59:22 2012 -0400
+++ b/splicesite.xml	Sun Apr 01 08:14:45 2012 -0400
@@ -7,6 +7,13 @@
         <option value="splicesitescore/score5.pl" selected="true">5' splice site</option>
         <option value="splicesitescore/score3.pl">3' splice site</option>
     </param>
+                <param name="genome" type="select" label="Select chromsome size file" >
+                <options from_file="chrsize.loc">
+                    <column name="name" index="0"/>
+                    <column name="value" index="1"/>
+                </options>
+            </param>
+            
   </inputs>
   <outputs>
     <data format="tabular" name="out_file1" />
diff -r 3fd430270c0c -r ec97befe722b splicesitescore/score3.pl
--- a/splicesitescore/score3.pl	Sun Apr 01 01:59:22 2012 -0400
+++ b/splicesitescore/score3.pl	Sun Apr 01 08:14:45 2012 -0400
@@ -4,8 +4,8 @@
 my $inputfile = $ARGV[0];
 my $usemaxent = 1;
 
-
-my @metables = &makemaxentscores;
+my $modelpath = "/home/wuxbl/rowley/tools/maxentscan/splicemodels/";
+my @metables = &makemaxentscores($modelpath);
 
 open (FILE,"<$inputfile") || die "can't open!\n";
 
@@ -51,7 +51,7 @@
 }
 
 sub makemaxentscores{
-    my $dir = "splicemodels/";
+    my $dir = shift;
     my @list = ('me2x3acc1','me2x3acc2','me2x3acc3','me2x3acc4',
 		'me2x3acc5','me2x3acc6','me2x3acc7','me2x3acc8','me2x3acc9');
     my @metables;
@@ -71,48 +71,7 @@
     }
     return @metables;
 }
-sub makewmmscores{
-    my $dir = "splicemodels/";
-    my @list = ('me1s0acc1','me1s0acc2','me1s0acc3','me1s0acc4',
-		'me1s0acc5','me1s0acc6','me1s0acc7','me1s0acc8','me1s0acc9');
-    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 makemmscores{
-    my $dir = "splicemodels/";
-    my @list = ('me2s0acc1','me2s0acc2','me2s0acc3','me2s0acc4',
-		'me2s0acc5','me2s0acc6','me2s0acc7','me2s0acc8','me2s0acc9');
-    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;
diff -r 3fd430270c0c -r ec97befe722b splicesitescore/score3.pl~
--- a/splicesitescore/score3.pl~	Sun Apr 01 01:59:22 2012 -0400
+++ b/splicesitescore/score3.pl~	Sun Apr 01 08:14:45 2012 -0400
@@ -4,8 +4,8 @@
 my $inputfile = $ARGV[0];
 my $usemaxent = 1;
 
-
-my @metables = &makemaxentscores;
+my $modelpath = "/home/wuxbl/rowley/tools/maxentscan/splicemodels/";
+my @metables = &makemaxentscores($modelpath);
 
 open (FILE,"<$inputfile") || die "can't open!\n";
 
@@ -51,7 +51,7 @@
 }
 
 sub makemaxentscores{
-    my $dir = "splicemodels/";
+    my $dir = shift;
     my @list = ('me2x3acc1','me2x3acc2','me2x3acc3','me2x3acc4',
 		'me2x3acc5','me2x3acc6','me2x3acc7','me2x3acc8','me2x3acc9');
     my @metables;
@@ -71,48 +71,7 @@
     }
     return @metables;
 }
-sub makewmmscores{
-    my $dir = "splicemodels/";
-    my @list = ('me1s0acc1','me1s0acc2','me1s0acc3','me1s0acc4',
-		'me1s0acc5','me1s0acc6','me1s0acc7','me1s0acc8','me1s0acc9');
-    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 makemmscores{
-    my $dir = "splicemodels/";
-    my @list = ('me2s0acc1','me2s0acc2','me2s0acc3','me2s0acc4',
-		'me2s0acc5','me2s0acc6','me2s0acc7','me2s0acc8','me2s0acc9');
-    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;
diff -r 3fd430270c0c -r ec97befe722b splicesitescore/score5.pl
--- a/splicesitescore/score5.pl	Sun Apr 01 01:59:22 2012 -0400
+++ b/splicesitescore/score5.pl	Sun Apr 01 08:14:45 2012 -0400
@@ -4,7 +4,7 @@
 my $inputfile = $ARGV[0];
 my $usemaxent = 1;
 
-my $modelpath = "splicesitescore/";
+my $modelpath = "/home/wuxbl/rowley/tools/maxentscan/";
 my %me2x5 = &makescorematrix($modelpath.'me2x5');
 my %seq = &makesequencematrix($modelpath.'splicemodels/splice5sequences');
 
diff -r 3fd430270c0c -r ec97befe722b splicesitescore/score5.pl~
--- a/splicesitescore/score5.pl~	Sun Apr 01 01:59:22 2012 -0400
+++ b/splicesitescore/score5.pl~	Sun Apr 01 08:14:45 2012 -0400
@@ -4,7 +4,7 @@
 my $inputfile = $ARGV[0];
 my $usemaxent = 1;
 
-my $modelpath = "/Users/xuebing/galaxy-dist/tools/mytools/splicesitescore/";
+my $modelpath = "/home/wuxbl/rowley/tools/maxentscan/splicemodels/";
 my %me2x5 = &makescorematrix($modelpath.'me2x5');
 my %seq = &makesequencematrix($modelpath.'splicemodels/splice5sequences');