1 files changed, 70 insertions, 0 deletions
diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch
new file mode 100644
index 0000000..cc07a98
--- /dev/null
+++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch
@@ -0,0 +1,70 @@
+--- meme_3.5.4/website/cgi-bin/meme.pl	2006-09-21 19:46:29.000000000 +0000
++++ trunk/website/cgi-bin/meme.pl	2007-09-10 00:28:33.000000000 +0000
+@@ -1,6 +1,6 @@
+ #!@WHICHPERL@
+ ##
+-## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $
++## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $
+ ##
+ ## $Log$
+ ## Revision 1.12  2006/03/07 23:30:19  nadya
+@@ -467,21 +467,21 @@
+ 
+   # check against allowed dna letters
+   $x = $_;
+-  $x =~ tr/ABCDGHKMNRSTUVWY//cd;
++  $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
+   $new = length $x;
+   if ($old == $new) {
+     "dna";
+   } else {
+     # check against allowed protein letters
+     $x = $_;
+-    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
++    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
+     $new = length $x;
+     if ($old == $new) {
+       "protein";
+     } else {
+       # get the unknown letters
+       $x = $_;
+-      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
++      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
+       &whine("
+ 	Your sequences contained the following unrecognized letters: $x.
+ 	<BR>
+--- meme_3.5.4/website/cgi-bin/mast.pl	2006-09-21 19:46:29.000000000 +0000
++++ trunk/website/cgi-bin/mast.pl	2007-09-10 00:38:14.000000000 +0000
+@@ -1,6 +1,6 @@
+ #!@WHICHPERL@
+ ##
+-## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $
++## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $
+ ##
+ ## $Log$
+ ## Revision 1.8  2006/03/07 23:30:19  nadya
+@@ -479,21 +479,21 @@
+ 
+   # check against allowed nucleotide letters
+   $x = $_;
+-  $x =~ tr/ABCDGHKMNRSTUVWY//cd;
++  $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
+   $new = length $x;
+   if ($old == $new) {
+     return("DNA");
+   } else {
+     # check against allowed protein letters
+     $x = $_;
+-    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
++    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
+     $new = length $x;
+     if ($old == $new) {
+       return("PROTEIN");
+     } else {
+       # get the unknown letters
+       $x = $_;
+-      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
++      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
+       &whine("
+         Your sequences contained the following unrecognized letters: $x.
+         <BR>