NAME

extract_bgc_sequences.pl - This script extracts protein sequences at several gene cluster levels and generates a FASTA file in output

VERSION

version 0.191620

NAME

extract_bgc_sequences.pl - This tool extracts sequences from Palantir (or antiSMASH) annotations and returns a FASTA file. The sequences may be extracted at different levels:

VERSION

This documentation refers to version 0.0.1

USAGE

        $0 [options] --paths <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).

--type [=] <str>

Filter cluster on a specific type. For instance: nrps, t1pks, t2pks, t3pks, nrps-t1pks, t1pks-nrps,...

OPTIONS

--annotation [=] <str>

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

--prefix [=] <str>

Prefix string to use in sequences ids (e.g., if Strain1: >Strain1@Cluster...)

--outfile [=] <outfile>

FASTA output filename.

--scale [=] <str>

Sequence scale to write in fasta: cluster, gene.

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

print the usual program information

AUTHOR

COPYRIGHT

AUTHOR

Loic MEUNIER <lmeunier@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.