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