NAME
Bio::BioStudio::GBrowse - GBrowse interaction
VERSION
Version 2.10
DESCRIPTION
BioStudio functions for interacting with GBrowse
AUTHOR
Sarah Richardson <smrichardson@lbl.gov>.
FUNCTIONS
add_to_GBrowse
remove_from_GBrowse
link_to_chromosome()
link_to_feature()
get_gbrowse_src_list()
Given the BioStudio config hashref, return a list of all of the chromosomes that are available through GBrowse
determine_feature_color()
INTERNALS
_path_to_GBrowse_dir
_path_to_conf
_path_to_repo
_server_address
_gbrowse_template
_path_to_colors
_dir_in_repository
_path_in_repository();
_create_chromosome_conf()
_add_to_GBrowse_conf()
_parse_gbrowse_colors()
get_cache_handle
STUBS
gbrowse_color_link()
Creates links to the gbrowse installation for genes
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.