Bio::Palantir::Refiner - front-end class for Bio::Palantir::Refiner module, wich handles the refinement of NRPS/PKS BGC annotations
version 0.191800
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
ClusterPlus.pm
GenePlus.pm: contains attributes and methods for the BGC Gene level, including an array of DomainPlus objects (if NRPS/PKS BGCs)
GenePlus.pm
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)
ModulePlus.pm
DomainPlus.pm: contains attributes and methods for the BGC Domain level
DomainPlus.pm
Path to biosynML.xml or regions.js antiSMASH report file to be parsed.
Path to a biosynML.xml or regions.js file
ArrayRef of Bio::Palantir::Refiner::ClusterPlus
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.
Returns all the Clusters of the Root (not an array reference).
# $root is a Bio::Palantir::Refiner::RootPlus my @clusters = $root->all_clusters;
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.
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).
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 # ... }
Loic MEUNIER <lmeunier@uliege.be>
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.
To install Bio::Palantir, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Palantir
CPAN shell
perl -MCPAN -e shell install Bio::Palantir
For more information on module installation, please visit the detailed CPAN module installation guide.