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--- 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-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
##
## $Log: meme-3.5.4-patch2.patch,v $
## Revision 1.1 2007/09/17 02:41:56 je_fro
## Add upstream patches and disable parallel install on amd64.
## (Portage version: 2.1.3.9)
##
## 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: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
##
## $Log: meme-3.5.4-patch2.patch,v $
## Revision 1.1 2007/09/17 02:41:56 je_fro
## Add upstream patches and disable parallel install on amd64.
## (Portage version: 2.1.3.9)
##
## 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>
|
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