Bio::Palantir::Parser - front-end class for Bio::Palantir::Parser module, wich handles the parsing of biosynML.xml and regions.js antiSMASH reports
version 0.191620
#TODO
This module implements classes and their methods for parsing antisMASH reports. The supported report formats are the biosynML.xml file generated in antiSMASH v3-4 (though the version 4 needs to be explicitely activated in the options) or the regions.js in the version 5.
The Biosynthetic Gene Cluster (BGC) information is hierarchically organized as follows:
Root.pm: contains the root of the BGC data structure
Root.pm
Cluster.pm: contains attributes and methods for the BGC Cluster level, including an array of Gene objects
Cluster.pm
Gene.pm: contains attributes and methods for the BGC Gene level, including an array of Domain objects (if NRPS/PKS BGCs)
Gene.pm
Module.pm: contains attributes and methods for the BGC Module level (generated by Palantir), including an array of Domain objects (this class is parallel to Genes, as module can be overlapping 2 genes)
Module.pm
domain.pm: contains attributes and methods for the BGC Domain level, including an array of Motif objects
domain.pm
Motif.pm: contains attributes and methods for the BGC Motif level
Motif.pm
Path to biosynML.xml or regions.js antiSMASH report file to be parsed.
Bio::Palantir::Parser::Root composed object
Bio::Palantir::Parser::Root
Path to a biosynML.xml or regions.js file
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.