NAME
extract_bgc_sequences.pl - Extracts protein sequences for different BGC scales into a FASTA file
VERSION
version 0.201670
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: cluster, gene, module and domain.
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]
- --module-delineation [=] <str>
-
Method for delineating the modules. Modules can either be cut on condensation (C and KS) or substrate-selection domains (A and AT) [default: 'substrate-selection'].
- --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.
- --prefix [=] <str>
-
Prefix string to use in sequences ids (e.g., if Strain1: >Strain1@Cluster...)
- --outfile [=] <filename>
-
FASTA output filename.
- --scale [=] <str>
-
BGC scale from which extracts sequences: cluster, gene, module and domain [default: gene].
- --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.