/ 
Bio-BioStudio-1.03
River stage zero No dependents
/ Bio::BioStudio::MySQL

NAME

BioStudio::MySQL

VERSION

Version 1.03

DESCRIPTION

BioStudio functions for MySQL interaction.

FUNCTIONS

list_databases() Given the BioStudio config hashref, return a hashref where the keys are all chromosomes available in the MySQL database.

create_database() Given a chromosome name and the BioStudio config hashref, create a mysql database to store the chromosome in MySQL. This function does not load the database!

load_database() Given a chromosome name, the BioStudio config hashref, and optionally, the name of an alternate chromosome, 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 chromosome provided unless the alternate is defined, in which case the alternate is loaded into a database named after the first chromosome.

fetch_database() Given a chromosome name and the BioStudio config hashref, returns a Bio::DB::SeqFeature::Store interface for the MySQL database containing the chromosome. An optional write flag sets whether or not the interface will support adding, deleting, or modifying features

drop_database() Given a chromosome name and the BioStudio config hashref, deletes the MySQL database containing the chromosome.

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

COPYRIGHT AND LICENSE

Copyright (c) 2011, 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. * Neither the name of the Johns Hopkins nor the names of the developers may 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.