CompBio::DB 0.47

CompBio::DB is a Perl module with methods for accessing data stored according to the CompBio base schema.

SYNOPSIS

use CompBio::DB;
my $cbdb = CompBio::DB->new({host => "foo.bar.edu");

my $AR_defs = $cbdb->get_annotation([keys %seqs]);
Example code for parsing the return for a simple print:
my $AR_result = $cbdb->get_aa_seq(@id_list);
foreach my $AR_row (@$AR_result) {
next unless @$AR_row;
print join("t",@$AR_row) , "n";
} # return list

This module and the related database schemas where developed to be used with a MySQL server. Although I would certainly prefer it to be portable, that was not a priority at this time. However, I expect the manual alterations that may be necisary to use this module should be very resonable for someone sufficiently familiar with the new target database server, and I would be happy to collaborate with anyone who wants to work on this!

Most of the methods in this database fetch a type of data from a given id or list of ids. Unless otherwise stated for a specific method, only two arguments are ever used; the id or an array reference to a list of ids, and a hash reference containing any optional arguments. The request will be made against the default database defined when the CompBio::DB object was created, but most methods accept a "database" option to use a different database on the same server.
All methods that return query results return a reference to a 2D array. See the documentaion for specific methods for the order of returned fields.