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Bio-GeneDesign-5.56
River stage zero No dependents
++
/ Bio::GeneDesign::PrefixTree

NAME

GeneDesign::PrefixTree - A suffix tree implementation for nucleotide searching

VERSION

Version 5.56

DESCRIPTION

  GeneDesign uses this object to parse peptide sequences for restriction enzyme
  recognition site possibilities

AUTHOR

Sarah Richardson <SMRichardson@lbl.gov>

Functions

new

Create a new suffix tree object.

    my $tree = Bio::GeneDesign::PrefixTree->new();

add_prefix

Add suffixes to the tree. You can add a sequence, an id (which can be an array reference of ids), and a scalar note.

    $tree->add_prefix('GGATCC', 'BamHI', "i hope this didn't pop up");
    $tree->add_prefix('GGCCC', ['OhnoI', 'WoopsII'], "I hope these pop up");

find_prefixes()

Pass a sequence to the tree and find the positions of hits. It will return an array that is made up of array references; each array reference represents a hit where the 0 index is the name of the subsequence in the tree, the 1 index is the offset in the query sequence (1 BASED, NOT 0 BASED), the 2 index is the subsequence, and the 3 index is whatever note is associated with the subsequence.

  my @hits = $tree->find_prefixes('AAAGGATCCATCGCATACGAGGCCCCACCG');

  # @hits = (['BamHI', 4, 'GGATCC', 'i hope this didn't pop up'],
  #          ['OhnoI', 21, 'GGCCC', 'I hope these pop up'],
  #          ['WoopsII', 21, 'GGCCC', 'I hope these pop up']
  #);

find_ntons

Pass a number, n. The tree will report all of the sequences inside it that it has only seen n times. The return value is a hash, where the keys are the sequences and the values are hash references containing the ids and notes associated with each sequence in the tree.

  my %twos = $tree->find_ntons(2);

  # %twos = ('GGGCC' => {'OhnoI' => ['I hope these pop up'],
  #                    'WoopsII' => ['I hope these pop up']}
  # );

COPYRIGHT AND LICENSE

Copyright (c) 2015, Sarah Richardson 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 GeneDesign 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.