NAME

generate_bgc_dnz_table.pl - Generates a denormalized table from BGC architectures

VERSION

version 0.191620

NAME

generate_bgc_dnz_table.pl - This tool parses and filters biosynthetic gene cluster information from antiSMASH results and resume it in a denormalized table.

VERSION

This documentation refers to the version 0.0.1

USAGE

        $0 [options] --path <biosynml_path> --taxdir <dir>

REQUIRED ARGUMENTS

--report[-file] [=] <infile>

Path to the output file of antismash, which can be either the biosynML.xml file (antiSMASH 3-4) or the regions.js (antiSMASH 5).

OPTIONS

--annotation [=] <str>

BGC annotation to use for extracting sequences. Annotations allowed: palantir or antismash [default: palantir]

--out <outfile>

TSV output filename. [default: bgc_output.tsv]

--type <str> ...

Filter the report for only a selection of biosynthetic gene cluster types. [default: none]

--id <str>

ID corresponding to the first column of the table. [default: directory/filename]

--version
--usage
--help
--man

print the usual program information

AUTHOR

Loic MEUNIER <lmeunier@uliege.be>

CONTRIBUTOR

Denis BAURAIN <denis.baurain@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.