NAME

generate_bgc_dnz_table.pl - Generates a denormalized table for BGC data

VERSION

version 0.200290

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.

USAGE

$0 [options] --report-file <infile>

REQUIRED ARGUMENTS

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

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

OPTIONAL ARGUMENTS

--annotation [=] <str>

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

--outfile [=] <filename>

TSV output filename. [default: bgc_data.tsv]

--types [=] <str>...

Filter clusters on a/several specific type(s).

Types allowed: acyl_amino_acids, amglyccycl, arylpolyene, bacteriocin, butyrolactone, cyanobactin, ectoine, hserlactone, indole, ladderane, lantipeptide, lassopeptide, microviridin, nrps, nucleoside, oligosaccharide, otherks, phenazine, phosphonate, proteusin, PUFA, resorcinol, siderophore, t1pks, t2pks, t3pks, terpene.

Any combination of these types, such as nrps-t1pks or t1pks-nrps, is also allowed. The argument is repeatable.

--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.