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Bio-BioStudio-2.11
River stage zero No dependents
++
/ Bio::BioStudio

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.