BioStudio functions for MySQL interaction.
Sarah Richardson <firstname.lastname@example.org>.
This function returns a hash reference containing all BioStudio database names as keys.
Arguments: The BioStudio configuration hashref
This function creates a MySQL database that is ready to be loaded with chromosome data. It does NOT load that database.
Arguments: A database name, the BioStudio configuration hashref
This function loads a MySQL database (which must have been previously created, see create_database()) with a GFF file. The file is the one corresponding to the first argument provided unless the alternate is defined, in which case the file corresponding to the third argument is loaded into a database named after the first argument.
Arguments: Database name as string BioStudio configuration hashref Optionally, the name of an alternate chromosome to be loaded using the database name provided in the first argument
Fetches a Bio::DB::SeqFeature::Store interface for a MySQL database containing the annotations of the argument chromosome. An optional write flag sets whether or not the interface will support adding, deleting, or modifying features.
Arguments: Database name BioStudio configuration hashref Optionally, a write flag Returns: A L<Bio::DB::SeqFeature::Store> object.
This function deletes a MySQL database.
Arguments: Database name BioStudio configuration hashref
Execute an arbitrary command on an arbitrary database
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