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| author |   Jeffrey Gardner <je_fro@gentoo.org> | 2007-10-14 00:03:28 +0000 |
|---|---|---|
| committer | Jeffrey Gardner <je_fro@gentoo.org> | 2007-10-14 00:03:28 +0000 |
| commit | 671c4b6fa357bd05ffafc2f3215218067f1f1fed (patch) | |
| tree | 4014e77bee3c2dc08392e373783bff70df6be816 /sci-biology/meme/files/meme-3.5.4-patch2.patch | |
| parent | Cleaning up and bumping to latest svn. (diff) | |
| download | je_fro-671c4b6fa357bd05ffafc2f3215218067f1f1fed.tar.gz je_fro-671c4b6fa357bd05ffafc2f3215218067f1f1fed.tar.bz2 je_fro-671c4b6fa357bd05ffafc2f3215218067f1f1fed.zip | |
Adding various packages so I can work on them later...
svn path=/; revision=87
Diffstat (limited to 'sci-biology/meme/files/meme-3.5.4-patch2.patch')
| -rw-r--r-- | sci-biology/meme/files/meme-3.5.4-patch2.patch | 78 |
1 files changed, 78 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..3854b83 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch @@ -0,0 +1,78 @@ +--- 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> |