NAME
Bio::Palantir::Parser - front-end class for Bio::Palantir::Parser module, wich handles the parsing of biosynML.xml and regions.js antiSMASH reports
VERSION
version 0.211420
SYNOPSIS
#TODODESCRIPTION
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
Cluster.pm: contains attributes and methods for the BGC Cluster level, including an array of Gene objects
Gene.pm: contains attributes and methods for the BGC Gene level, including an array of Domain objects (if NRPS/PKS BGCs)
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)
domain.pm: contains attributes and methods for the BGC Domain level, including an array of Motif objects
Motif.pm: contains attributes and methods for the BGC Motif level
ATTRIBUTES
file
Path to biosynML.xml or regions.js antiSMASH report file to be parsed.
root
Bio::Palantir::Parser::Root composed object
file
Path to a biosynML.xml or regions.js file
root
Bio::Palantir::Parser::Root composed object
module_delineation
Module delineation method: generates modules from condensation or selection domains.
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.