Sarah Richardson > Bio-BioStudio-2.00 > Bio::BioStudio

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NAME ^

Bio::BioStudio

VERSION ^

Version 2.00

DESCRIPTION ^

AUTHOR ^

Sarah Richardson <smrichardson@lbl.gov>

CONSTRUCTORS ^

new

 Title   : new
 Function:
 Returns : a new Bio::BioStudio object
 Args    :

FUNCTIONS ^

ACCESSORS ^

path_to_markers

path_to_repo

path_to_features

tmp_path

script_path

gbrowse

cairo

bioperl_path

conf

FUNCTIONS ^

set_chromosome

gather_latest_genome

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

species_list

source_list

db_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.

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.

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