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Bio-Palantir-0.191800
River stage zero No dependents
1 ++

Changes for version 0.191800 - 2019-06-29

  • Additions
    • documentation: added Manual.pod
    • Roles::Domainable: added a class attribute
    • Parser: added is_cluster_type_ok method
  • Changes
    • binaries: renamed '--type' option in '--types' (repeatable argument)
    • binaries: improved the '--help' documentation
    • Roles::Fillable: removed _get_class method
  • Fixes
    • all: fixed minor bugs

Documentation

Manual
draw_bgc_maps.pl
This script draws NRPS/PKS BGC clusters maps in PNG
explore_bgc_domains.pl
Reports all detected domain signatures for a NRPS/PKS gene cluster
export_bgc_sql_tables.pl
Exports SQL tables of BGC data (Palantir and antiSMASH annotations)
extract_bgc_sequences.pl
Extracts protein sequences for different BGC scales into a FASTA file
generate_bgc_dnz_table.pl
Generates a denormalized table for BGC data
generate_bgc_report.pl
Generates PDF/Word reports from antiSMASH results

Modules

Bio::Palantir
core classes and utilities for Bio::Palantir
Bio::Palantir::Explorer
front-end class for Bio::Palantir::Explorer module, wich handles the NRPS/PKS domain exploration without pre-existing consensus architecture
Bio::Palantir::Explorer::ClusterFasta
Explorer internal class for handling ClusterFasta objects
Bio::Palantir::Explorer::GeneFasta
Explorer internal class for handling GeneFasta objects
Bio::Palantir::Parser
front-end class for Bio::Palantir::Parser module, wich handles the parsing of biosynML.xml and regions.js antiSMASH reports
Bio::Palantir::Parser::Cluster
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Domain
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Gene
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Location
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Motif
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Qualifier
BiosynML DTD-derived internal class
Bio::Palantir::Parser::Root
BiosynML DTD-derived internal class
Bio::Palantir::Refiner
front-end class for Bio::Palantir::Refiner module, wich handles the refinement of NRPS/PKS BGC annotations
Bio::Palantir::Refiner::ClusterPlus
Refiner internal class for handling ClusterPlus objects
Bio::Palantir::Refiner::DomainPlus
Refiner internal class for handling DomainPlus objects
Bio::Palantir::Refiner::GenePlus
Refiner internal class for handling GenePlus objects
Bio::Palantir::Roles::Clusterable
Clusterable Moose role for Cluster and ClusterPlus objects
Bio::Palantir::Roles::Domainable
Domainable Moose role for Domain and DomainPlus objects
Bio::Palantir::Roles::Fillable
Fillable Moose role for the construction of DomainPlus object arrays and Exploratory methods
Bio::Palantir::Roles::Geneable
Geneable Moose role for Gene and GenePlus objects
Bio::Palantir::Roles::Modulable
Modulable Moose role for Module object construction
Bio::Palantir::Roles::Modulable::Module
BiosynML DTD-derived internal class

Other files