1#!/usr/bin/perl -w 2 3use Cwd; 4 5%dbformats = ("embl" => "embl", 6 "genbank" => "genbank", 7 "swiss" => "swissprot", 8 "wormpep" => "fasta"); 9 10%dbfiles = ("embl" => "*.dat", 11 "genbank" => "*.seq", 12 "swiss" => "*.dat", 13 "wormpep" => "wormpep"); 14 15$distribtop = "/home/pmr/devemboss"; 16 17#open (VERS, "embossversion -full -auto|") || die "Cannot run embossversion"; 18#while (<VERS>) { 19# if(/InstallDirectory: +(\S+)/) { 20# $installtop = $1; 21# $installtop =~ s/\/$//; 22# } 23# if(/BaseDirectory: +(\S+)/) { 24# $distribtop = $1; 25# $distribtop =~ s/\/$//; 26# } 27#} 28#close VERS; 29 30foreach $db (sort(keys(%dbformats))) { 31 chdir ("$distribtop/test/$db"); 32 printf "$db: %s\n", cwd(); ; 33 $location = "$db"; 34 if($db eq "wormpep") {$location = "worm"} 35 elsif($db eq "swiss") {$location = "swissprot"} 36 $format = $dbformats{$db}; 37 $dbfiles = $dbfiles{$db}; 38 system "mv $location/CVS ./savecvs"; 39 print STDERR "~/devemboss/scripts/bioflat_index_obda.pl --create --indextype flat --dbname $location --location . --format $format $dbfiles\n"; 40 system "~/devemboss/scripts/bioflat_index_obda.pl --create --indextype flat --dbname $location --location . --format $format $dbfiles"; 41 system "mv ./savecvs $location/CVS"; 42} 43