Use Bio::DB::GFF->new() to construct new instances of this class.
Three named arguments are recommended:
-adaptor Set to "berkeleydb" to create an instance of this class.
-dsn Path to directory where the database index files will be stored (alias -db)
-autoindex Monitor the indicated directory path for FASTA and GFF files, and update the
indexes automatically if they change (alias -dir)
-write Set to a true value in order to update the database.
-create Set to a true value to create the database the first time
-tmp Location of temporary directory for storing intermediate files
during certain queries.
-preferred_groups Specify the grouping tag. See L<Bio::DB::GFF>
The -dsn argument selects the directory in which to store the database
index files. If the directory does not exist it will be created
automatically, provided that the current process has sufficient
privileges. If no -dsn argument is specified, a database named test
will be created in your systems temporary files directory.
The -tmp argument specifies the temporary directory to use for storing
intermediate search results. If not specified, your systems temporary
files directory will be used. On Unix systems, the TMPDIR environment
variable is honored. Note that some queries can require a lot of
The -autoindex argument, if present, selects a directory to be
monitored for GFF and FASTA files (which can be compressed with the
gzip program if desired). Whenever any file in this directory is
changed, the index files will be updated. Note that the indexing can
take a long time to run: anywhere from 5 to 10 minutes for a million
features. An alias for this argument is -dir, which gives this adaptor
a similar flavor to the memory adaptor.
-dsn and -dir can point to the same directory. If -dir is given but
-dsn is absent the index files will be stored into the directory
containing the source files. For autoindexing to work, you must
specify the same -dir path each time you open the database.
If you do not choose autoindexing, then you will want to load the
database using the bp_load_gff.pl command-line tool. For example:
bp_load_gff.pl -a berkeleydb -c -d /usr/local/share/gff/dmel dna1.fa dna2.fa features.gff