Sarah Richardson > Bio-BioStudio-1.05 > Bio::BioStudio::GBrowse

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Module Version: 1.05   Source   Latest Release: Bio-BioStudio-2.00

NAME ^

Bio::BioStudio::GBrowse - GBrowse interaction

VERSION ^

Version 1.05

DESCRIPTION ^

BioStudio functions for GBrowse

AUTHOR ^

Sarah Richardson <notadoctor@jhu.edu>.

Functions ^

gbrowse_gene_names()

  Creates links to the gbrowse installation for genes

make_link()

Given a list of Bio::SeqFeature gene objects, a BioStudio parameter hashref, and the BioStudio config hashref, generate a hashref such that the key is the gene id and the value is a display friendly link to GBrowse.

get_gbrowse_src_list()

Given the BioStudio config hashref, return a list of all of the chromosomes that are available through GBrowse

write_conf_file()

Given the BioStudio config hashref, the name of the chromosome, and a note, create a configuration file by replacing values in the BioStudio template of a GBrowse conf file.

update_gbrowse()

Given a BioStudio config hashref and a BioStudio parameter hashref, update GBrowse - reload the database, write the configuration file, and pass a link.

rollback_gbrowse()

Given a BioStudio config hashref and a BioStudio parameter hashref, remove a source from GBrowse.

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.

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