/ 
Bio-Palantir-0.211420
River stage zero No dependents
/ Bio::Palantir::Refiner

NAME

Bio::Palantir::Refiner - front-end class for Bio::Palantir::Refiner module, wich handles the refinement of NRPS/PKS BGC annotations

VERSION

version 0.211420

DESCRIPTION

This module implements classes and their methods for improving the antisMASH annotation of NRPS/PKS BGCs.

The refined Biosynthetic Gene Cluster (BGC) information is hierarchically organized as follows:

ClusterPlus.pm: contains attributes and methods for the BGC Cluster level, including an array of GenePlus objects

GenePlus.pm: contains attributes and methods for the BGC Gene level, including an array of DomainPlus objects (if NRPS/PKS BGCs)

ModulePlus.pm: contains attributes and methods for the BGC Module level (generated by Palantir), including an array of DomainPlus objects (this class is parallel to Genes, as module can be overlapping 2 genes)

DomainPlus.pm: contains attributes and methods for the BGC Domain level

ATTRIBUTES

file

Path to biosynML.xml or regions.js antiSMASH report file to be parsed.

file

Path to a biosynML.xml or regions.js file

module_delineation

Module delineation method: generates modules from condensation or selection domains.

clusters

ArrayRef of Bio::Palantir::Refiner::ClusterPlus

METHODS

count_clusters

Returns the number of Clusters of the Root.

# $root is a Bio::Palantir::Refiner::RootPlus
my $count = $root->count_clusters;

This method does not accept any arguments.

all_clusters

Returns all the Clusters of the Root (not an array reference).

# $root is a Bio::Palantir::Refiner::RootPlus
my @clusters = $root->all_clusters;

This method does not accept any arguments.

get_cluster

Returns one Cluster of the Root by its index. You can also use negative index numbers, just as with Perl's core array handling. If the specified Cluster does not exist, this method will return undef.

# $root is a Bio::Palantir::Refiner::RootPlus
my $cluster = $root->get_cluster($index);
croak "Cluster $index not found!" unless defined $cluster;

This method accepts just one argument (and not an array slice).

next_cluster

Shifts the first Cluster of the array off and returns it, shortening the array by 1 and moving everything down. If there are no more Clusters in the array, returns undef.

# $root is a Bio::Palantir::Refiner::RootPlus
while (my $cluster = $root->next_cluster) {
    # process $cluster
    # ...
}

This method does not accept any arguments.

AUTHOR

Loic MEUNIER <lmeunier@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2019 by University of Liege / Unit of Eukaryotic Phylogenomics / Loic MEUNIER and Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.