1 files changed, 0 insertions, 70 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
deleted file mode 100644
index cc07a98..0000000
--- a/sci-biology/meme/files/meme-3.5.4-patch2.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- 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>