NAME
Bio::BioStudio
VERSION
Version 2.10
DESCRIPTION
AUTHOR
Sarah Richardson <smrichardson@lbl.gov>
CONSTRUCTORS
new
Title : new
Function:
Returns : a new Bio::BioStudio object
Args :FUNCTIONS
ACCESSORS
path_to_markers
custom_markers
path_to_repo
path_to_features
custom_features
tmp_path
script_path
gbrowse
SGE
BLAST
cairo
bioperl_path
conf
FUNCTIONS
set_chromosome
gather_latest_genome
get_species_BLAST_database
BLASTn_short_sequence
species_list
source_list
gv_increment_warning
cv_increment_warning
prepare_repository
ACCESSORS
genome_repository
A path to a directory that can be used as a genome repository. Defaults to the config dir as set at install slash genome_repository.
db_engine
A path to a directory that can be used as a genome repository. Defaults to the config dir as set at install slash genome_repository.
_fetch_custom_features()
Returns a hashref of custom features in the BioStudio configuration directory. Each key is a feature name, each value is a Bio::SeqFeature object.
_fetch_custom_markers
_import_fasta
DESTROY
COPYRIGHT AND LICENSE
Copyright (c) 2013, 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 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.