NAME
Bio::BioStudio::Chromosome
VERSION
Version 2.10
DESCRIPTION
AUTHOR
Sarah Richardson <smrichardson@lbl.gov>
CONSTRUCTORS
new
Title : new
Function:
Returns : a new Bio::BioStudio::Chromosome object
Args :DESTROY
FUNCTIONS
ACCESSORS
provisional
Provisional databases are removed from the repository and the db engine when the programs shut down.
name
repo
path_to_GFF
path_to_DB
path_in_repo
gbrowse
database
db
container_id
feature_mask
type_mask
empty_mask
species
genome_version
chromosome_version
tag
seq_id
chromosome_id
signature
sequence
len
seqobj
comments
add_to_comments
add_reason
GD
FUNCTIONS
rollback
fetch_comments
fetch_features
add_feature
modify_feature
Check if sequence requires moving things downstream
insert_feature
delete_region
flatten_subfeats
Given a seqfeature, iterate through its subfeatures and add all their subs to one big array. Mainly need this when CDSes are hidden behind mRNAs in genes.
current_sequence
make_cDNA
make_intergenic_features
iterate
Creates a PROVISIONAL copy of the current chromosome.today
write_chromosome
allowable_codon_changes()
Given two codons (a from, and a to) and a GeneDesign codon table hashref, this function generates every possible peptide pair that could contain the from codon and checks to see if the peptide sequence can be maintained when the from codon is replaced by the to codon. This function is of particular use when codons are being changed in genes that overlap one another.
print_comments
genbank_feature
FASTA
gff3
gff3_string
analyze_proteinCodingGenes
analyze_RestrictionEnzymes
analyze_ArbitraryFeatures
gbrowse_feature_link
gbrowse_chromosome_link
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.