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| author |   Gunnar Wrobel <wrobel@gentoo.org> | 2005-01-19 09:12:37 +0000 |
|---|---|---|
| committer | Gunnar Wrobel <wrobel@gentoo.org> | 2005-01-19 09:12:37 +0000 |
| commit | ed04783f06d65268fe0e42427d2bd034a110744e (patch) | |
| tree | da148d69bd092f04e8e634f82067a1e51b8c8381 /sci-biology | |
| parent | fixed permissions on repbase ebuild (diff) | |
| download | overlay-ed04783f06d65268fe0e42427d2bd034a110744e.tar.gz overlay-ed04783f06d65268fe0e42427d2bd034a110744e.tar.bz2 overlay-ed04783f06d65268fe0e42427d2bd034a110744e.zip | |
Fixed cleaning script
svn path=/; revision=80
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/repbase/Manifest | 2 | ||||
| -rwxr-xr-x | sci-biology/repbase/files/clean | 45 |
2 files changed, 25 insertions, 22 deletions
diff --git a/sci-biology/repbase/Manifest b/sci-biology/repbase/Manifest index b15779e..68741b4 100644 --- a/sci-biology/repbase/Manifest +++ b/sci-biology/repbase/Manifest @@ -1,3 +1,3 @@ MD5 91b78f561ed7a033faf48d1e4d5c68e3 repbase-9.12.ebuild 1456 -MD5 5de6ba25014bec88b60fa472c4b69a91 files/clean 1120 +MD5 943163c2456b74490a384738b63d6d94 files/clean 1161 MD5 6d171b2224c472ad2ab93a3033b09c96 files/digest-repbase-9.12 70 diff --git a/sci-biology/repbase/files/clean b/sci-biology/repbase/files/clean index b681d52..37ee59c 100755 --- a/sci-biology/repbase/files/clean +++ b/sci-biology/repbase/files/clean @@ -15,36 +15,39 @@ while (<LIB>) { if (m/^>/) { - if ($sequence eq "" and not $name eq "") + if (not $name eq "") { - print "---------------------------------------------------------------------------------------\n"; - print "Empty sequence: " . $name . "\n"; - } - else - { - if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/) + if ($sequence eq "") + { + print "---------------------------------------------------------------------------------------\n"; + print "Empty sequence: " . $name . "\n"; + } + else { - $sequence =~ s/[WSYRMHKXDVB]/N/g; - if (not $sequence =~ m/NNNN/) + if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/) { - print CLIB $name; - print CLIB $sequence . "\n"; + $sequence =~ s/[WSYRMHKXDVB]/N/g; + if (not $sequence =~ m/NNNN/) + { + print CLIB $name; + print CLIB $sequence . "\n"; + } + else + { + print "---------------------------------------------------------------------------------------\n"; + print "Too many N's: " . $name; + } } else { print "---------------------------------------------------------------------------------------\n"; - print "Too many N's: " . $name; + print "Invalid entry: " . $name; + $sequence =~ s/[ACGTN]//g; + print "Reduced sequence:\n"; + print $sequence . "\n"; } + $sequence = ""; } - else - { - print "---------------------------------------------------------------------------------------\n"; - print "Invalid entry: " . $name; - $sequence =~ s/[ACGTN]//g; - print "Reduced sequence:\n"; - print $sequence . "\n"; - } - $sequence = ""; } $name = $_; } |