NAME

generate_bgc_report.pl - Generates PDF/Word reports from antiSMASH results

VERSION

version 0.211420

NAME

generate_bgc_report.pl - Parses and filters biosynthetic gene cluster information from antiSMASH analyses and report these in PDF or docx reports

USAGE

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

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

--filetype [=] <str>

Your report can be either in PDF or Word docx format. Choose pdf or docx [default: pdf].

--outfile [=] <filename>

Output filename [default: bgc_report].

--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.

--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.