This is a lazy but easy way to get the db-related arguments. All you
need to do is to invoke get_ens_db_from_argv before using standard
Getopt. The below options will be absorbed and removed from @ARGV.
db_file, host, db_host, dbhost, user, db_user, dbuser, pass, db_pass,
dbpass, dbname, db_name.
Now you can take advantage of Perl's do method to execute a file as perl
script and get returned the last line of it. For your most accessed db
setting, you can have a file named, say, ensdb_homo_core_18.perlobj,
with the content like
use strict; # The ceiling line
use Bio:: EnsEMBL::DBSQL::DBAdaptor;
my $db = Bio:: EnsEMBL::DBSQL::DBAdaptor->new(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-dbname => 'homo_sapiens_core_18_34'
);
$db; # The floor line
In the your command line, you just need to write like
perl my_script.pl -db_file ensdb_homo_core_18.perlobj
rather than the verbose
-host ensembldb.ensembl.org -user anonymous \
-dbname homo_sapiens_core_18_34
None available.
sub get_ens_db_from_argv
{ my ($db_file, $host, $user, $pass, $dbname, $driver, $db_module);
$host = 'localhost';
$driver ='mysql';
$db_module = 'Bio::EnsEMBL::SQL::DBAdaptor';
Getopt::Long::config('pass_through');
&GetOptions(
'db_file=s' =>\$ db_file,
'driver|dbdriver|db_driver=s' =>\$ driver,
'host|dbhost|db_host=s' =>\$ host,
'user|dbuser|db_user=s' =>\$ user,
'pass|dbpass|db_pass=s' =>\$ pass,
'dbname|db_name=s' =>\$ dbname,
'db_module=s' =>\$ db_module
);
my $db;
if(defined $db_file){
-e $db_file or die "'$db_file' is defined but does not exist\n";
eval { $db = do($db_file) };
$@ and die "'$db_file' is not a perlobj file\n";
$db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')
or die "'$db_file' is not EnsEMBL DBAdaptor\n";
_debug_print "I get a db from file\n";
}elsif(defined $host and defined $user and defined $dbname){
Bio::Root::Root::_load_module($db_module);
$db = $db_module->new(
-host => $host,
-user => $user,
-pass => $pass,
-dbname => $dbname,
-driver => $driver
);
}else{
die "Cannot get the db, due to the insufficient information\n";
}
return $db;} |