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Bio-BioStudio-1.05
River stage zero No dependents
++
/ Bio::BioStudio::MySQL

NAME

Bio::BioStudio::MySQL

VERSION

Version 1.05

DESCRIPTION

BioStudio functions for MySQL interaction.

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

list_databases

This function returns a hash reference containing all BioStudio database names as keys.

  Arguments: The BioStudio configuration hashref

create_database

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

load_database

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

fetch_database

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.

drop_database

This function deletes a MySQL database.

  Arguments: Database name
             BioStudio configuration hashref

db_execute

Execute an arbitrary command on an arbitrary database

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.