[med-svn] r2131 - trunk/community/infrastructure/getData

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-07-03 22:56:29 +0000 (Thu, 03 Jul 2008)
New Revision: 2131

Modified:
   trunk/community/infrastructure/getData/getData
Log:
SWISS-PROT works.


Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData	2008-07-03 13:49:11 UTC (rev 2130)
+++ trunk/community/infrastructure/getData/getData	2008-07-03 22:56:29 UTC (rev 2131)
@@ -236,8 +236,8 @@
 		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz ftp://ftp.ebi.ac.uk/pub/databases/swissprot/updates_compressed/*.dat.gz",
 		"post-download" => "d=uncompressed; if [ ! -d \$d ]; then mkdir \$d; fi; "
 				  ."rm -rf \$d/swissprot.dat; "
-				  ."(tfind ftp.ebi.ac.uk -name '*.dat.gz` | xargs -r zcat ) > \$d/swissprot.dat; "
-				  ."[ -x /usr/bin/dbiflat ] && cd \$d && dbiflat -dbresource embl -dbname swisslocal -fields acc,des -auto"
+				  ."(find ftp.ebi.ac.uk -name '*.dat.gz' | xargs -r zcat ) > \$d/swissprot.dat; "
+				  ."[ -x /usr/bin/dbiflat ] && cd \$d && dbiflat -dbname swisslocal -fields acc,des -idformat swiss -auto"
 	#	source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz"
 	},
 
@@ -343,6 +343,10 @@
 	}
 
 	if ($do_config) {
+
+		die "Please specify a system to configure.\n"
+			unless 0<length(@$config);
+
 		foreach my $system (@$config) {
 			if ("emboss" eq "$system") {
 				if ($db =~ /(swiss|trembl).dat/ ) {
@@ -376,7 +380,7 @@
 					print "MIRRORDIR=\"$mirrordir\"\n";
 				}
 				else {
-					print STDERR "$db: not installed, configuration not printed.
+					print STDERR "$db: not installed, configuration not printed.";
 				}
 			}
 			else {