Introduction to AcePerl
AcePerl is an excellent Perlmodule which provides access to ACeDB databases, and is written by Lincoln Stein, who also wrote CGI.pm.
AcePerl is an object-oriented Perl module, so you
need to be happy with object-oriented Perl to use it. AcePerl can be used
to access ACeDB databases either by contacting anaceserver
directly, or by wrapping atace
process opened on an ACeDB database directory. Access
through the server is usually faster and more reliable.
There are two principal types of object in AcePerl, Database handle objects andData objects.
Database handle objects
These are connections to ACeDB databases. A conection
is made with the connect()method. This
example script opens a connection, and stores it in the variable$db:
#!/usr/local/bin/perl -w
use strict;
use Ace; # Import the AcePerl library
my $host = 'humsrv1';
my $port = 310000;
my $db = Ace->connect( -host => $host, -port => $port )
or die "Can't connect to '$host' on port '$port' : ", Ace->error;
Data objects
Fetching objects from the database
Once you have a connection to the ACeDB database,
objects can be retrieved from it using thefetch() method:
my $seq = $db->fetch(Sequence => 'bK390B3')
or die "Can't fetch sequence 'bK390B3'";
Accessing tags in the object
The object's data tree can be accessed with the
at() method. It is very helpful to have
xace open on the model or example data
at this stage!
my $author = $seq->at('Origin.From_Author[1]');
print "Author of $seq is $author\n";
This call fetches the tag one hop to the right (specified
by '[1]') of theFrom_Author tag. The full path to the tag through the object (ie: via
Origin) must be specified with theat()
method.
IMPORTANT: Everything is an object
Everything which you get from a database with AcePerl
is an object. These objects automatically convert themselves into a string
when called in a string context (in the print statement above for example).
What actually happens internally is that thename() method
is called on the object.
This can trap you when you store data retrieved
with AcePerl in your Perl script (in a hash for example), because you can
rapidly run out of memory as you accumulate numbers of large AcePerl objects.
If, for instance, you stored the $author object above, then what you actually store is a full AcePerl object,
which knows which Class it belongs to and contains a handle to its database.
To store just the string, you need to callname()
directly, or put it in string context:
my( %seq_authors ); # For storing the author of each sequence
# These two lines are equivalent:
$seq_authors{$seq} = "$author";
$seq_authors{$seq} = $author->name;
# ($seq gets stringified because hash keys
# force string context.)
Getting lists of tags
Called in array context, the at()
method returns a list of objects. The following piece
of code gets the column of sequence object tags to the right of the
Subsequencetag, and then uses the
row() method to get the two tags one hop
to the right:
my @sub_list = $seq->at('Structure.Subsequence[1]');
foreach my $subseq (@sub_list) {
my($left, $right) = $subseq->row(1);
print "Subsequence: $subseq\t$left\t$right\n";
}