NAME
Bio::BioStudio::DB::MySQL
VERSION
Version 2.10
DESCRIPTION
BioStudio functions for MySQL database interaction.
AUTHOR
Sarah Richardson <SMRichardson@lbl.gov>.
DATABASE FUNCTIONS
_prefix
_realname
_pass
_host
_port
_user
_connectstring
_dbh
_database_exists
_fetch_database
Fetches a Bio::DB::SeqFeature::Store interface for a 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.
Returns: A L<Bio::DB::SeqFeature::Store> object._list_databases
This function returns a hash reference containing all BioStudio database names as keys.
_create_database
This function creates a database that is ready to be loaded with chromosome data. It does NOT load that database.
_load_database
This function loads a 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: Optionally, the name of an alternate chromosome to be loaded using
the database name provided in the first argument_drop_database
This function drops the database associated with a BioStudio chromosome.
db_execute
Execute an arbitrary command on an arbitrary database
db_search
Execute a search command on an arbitrary database
COPYRIGHT AND LICENSE
Copyright (c) 2015, BioStudio developers All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* The names of Johns Hopkins, the Joint Genome Institute, the Joint BioEnergy Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the BioStudio developers may not be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.