NAME

Bio::Coordinate::Graph - Finds shortest path between nodes in a graph.

VERSION

version 1.007001

SYNOPSIS

# get a hash of hashes representing the graph. E.g.:
my $hash= {
           '1' => {
                   '2' => 1
                  },
           '2' => {
                   '4' => 1,
                   '3' => 1
                  },
           '3' => undef,
           '4' => {
                   '5' => 1
                  },
           '5' => undef
          };

# create the object;
my $graph = Bio::Coordinate::Graph->new(-graph => $hash);

# find the shortest path between two nodes
my $a = 1;
my $b = 6;
my @path = $graph->shortest_paths($a);
print join (", ", @path), "\n";

DESCRIPTION

This class calculates the shortest path between input and output coordinate systems in a graph that defines the relationships between them. This class is primarely designed to analyze gene-related coordinate systems. See Bio::Coordinate::GeneMapper.

Note that this module can not be used to manage graphs.

Technically the graph implemented here is known as Directed Acyclic Graph (DAG). DAG is composed of vertices (nodes) and edges (with optional weights) linking them. Nodes of the graph are the coordinate systems in gene mapper.

The shortest path is found using the Dijkstra's algorithm. This algorithm is fast and greedy and requires all weights to be positive. All weights in the gene coordinate system graph are currently equal (1) making the graph unweighted. That makes the use of Dijkstra's algorithm an overkill. A simpler and faster breadth-first would be enough. Luckily the difference for small graphs is not significant and the implementation is capable of taking weights into account if needed at some later time.

Input format

The graph needs to be primed using a hash of hashes where there is a key for each node. The second keys are the names of the downstream neighboring nodes and values are the weights for reaching them. Here is part of the gene coordiante system graph:

$hash = {
         '6' => undef,
         '3' => {
                 '6' => 1
                },
         '2' => {
                 '6' => 1,
                 '4' => 1,
                 '3' => 1
                },
         '1' => {
                 '2' => 1
                },
         '4' => {
                 '5' => 1
                },
         '5' => undef
        };

Note that the names need to be positive integers. Root should be '1' and directness of the graph is taken advantage of to speed calculations by assuming that downsream nodes always have larger number as name.

An alternative (shorter) way of describing input is to use hash of arrays. See Bio::Coordinate::Graph::hash_of_arrays.

METHODS

new

graph

Title   : graph
Usage   : $obj->graph($my_graph)
Function: Read/write method for the graph structure
Example :
Returns : hash of hashes grah structure
Args    : reference to a hash of hashes

hash_of_arrays

Title   : hash_of_arrays
Usage   : $obj->hash_of_array(%hasharray)
Function: An alternative method to read in the graph structure.
          Hash arrays are easier to type. This method converts
          arrays into hashes and assigns equal values "1" to
          weights.

Example : Here is an example of simple structure containing a graph.

          my $DAG = {
                     6  => [],
                     5  => [],
                     4  => [5],
                     3  => [6],
                     2  => [3, 4, 6],
                     1  => [2]
                    };

Returns : hash of hashes graph structure
Args    : reference to a hash of arrays

shortest_path

Title   : shortest_path
Usage   : $obj->shortest_path($a, $b);
Function: Method for retrieving the shortest path between nodes.
          If the start node remains the same, the method is sometimes
          able to use cached results, otherwise it will recalculate
          the paths.
Example :
Returns : array of node names, only the start node name if no path
Args    : name of the start node
        : name of the end node

dijkstra

Title   : dijkstra
Usage   : $graph->dijkstra(1);
Function: Implements Dijkstra's algorithm.
          Returns or sets a list of mappers. The returned path
          description is always directed down from the root.
          Called from shortest_path().
Example :
Returns : Reference to a hash of hashes representing a linked list
          which contains shortest path down to all nodes from the start
          node. E.g.:

           $res = {
                     '2' => {
                              'prev' => '1',
                              'dist' => 1
                            },
                     '1' => {
                              'prev' => undef,
                              'dist' => 0
                            },
                   };

Args    : name of the start node

FEEDBACK

Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/%%7Bdist%7D

AUTHOR

Heikki Lehvaslaiho <heikki@bioperl.org>

COPYRIGHT

This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

cpanm Bio::Coordinate

perl -MCPAN -e shell
install Bio::Coordinate