Changes for version 0.193230 - 2019-11-19
- Additions
- Added module delineation option in bin/ scripts
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
- Changes
- INSTALL
- LICENSE
- MANIFEST
- META.yml
- Makefile.PL
- README
- example_data/Streptomyces_coelicolor_A3_Cluster10.js
- example_data/results/bgc_db
- example_data/results/bgc_db_tables/Clusters
- example_data/results/bgc_db_tables/Domains
- example_data/results/bgc_db_tables/Domains_explus
- example_data/results/bgc_db_tables/Domains_plus
- example_data/results/bgc_db_tables/Genes
- example_data/results/bgc_db_tables/Genes_plus
- example_data/results/bgc_db_tables/Lineages
- example_data/results/bgc_db_tables/Modules
- example_data/results/bgc_db_tables/Modules_plus
- example_data/results/bgc_db_tables/Sequences
- example_data/results/bgc_maps/Cluster1_NRPS.png
- example_data/results/cluster10_denormalized_table.tsv
- example_data/results/cluster10_gene_sequences.fasta
- example_data/results/load_db.sql