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.