NRPS-rs: A Rust reimplementation of NRPSPredictor2

This is an (almost) feature-for-feature reimplementation of NRPSPredictor2 in Rust. On the SVM side of things, it loads the same mdl files with feature vectors and produces the same scores. The Stachelhaus tables have been updated with all the signature/substrate mappings from the MIBiG 3.1 release. The output text format is slightly different, as NRPS-rs adds an additional 8 Å signature lookup to differentiate between results with identical Stachelhaus signatures.

Installation

NRPS-rs is available via cargo, so the easiest way to install it is to run

cargo install nrps-rs

Alternatively, you can clone the git repository and run

cargo build -r

and then copy the resulting binary from target/release/nrps-rs into your $PATH.

Data

In order to actually run NRPS-rs, you'll need to provide a Stachelhaus signature file and SVM model files. You can fetch the ones antiSMASH uses from https://dl.secondarymetabolites.org/releases/stachelhaus/1.1/ and https://dl.secondarymetabolites.org/releases/nrps_svm/2.0/

NRPS-rs looks in $PWD/data/models by default, but you can set alternative locations using the --model-dir (and --stachelhaus-signatures) parameters or the config file.

Configuration

NRPS-rs can be configured via command line parameters or a config file. By default, NRPS-rs looks for a file named nrps.toml in the current working directory, this can be overridden by the --config parameter.

Running NRPS-rs

To run NRPS-rs, you need to provide an input file containing the 8 Å active site signature of the adenylation domain(s) you want to predict, with one line per A domain containing the 34 AA signature and an identifier for the domain, separated by a tab.

Example

This example assumes you have the antiSMASH models and signatures installed as described above. We use --skip-v3 because the antiSMASH model set doesn't provide the experimental third generation models but sticks with the original NRPSPredictor2 ones.

echo -e "LDASFDASLFEMYLLTGGDRNMYGPTEATMCATW\tbpsA" > example.sigs
nrps-rs --skip-v3 example.sigs
Name	8A signature	Stachelhaus signature	Full Stachelhaus match	AA10 score	AA10 signature matched	AA34 score	Stachelhaus	ThreeClusterV2	LargeClusterV2	SmallClusterV2	SingleV2	LargeClusterV1	SmallClusterV1
bpsA	LDASFDASLFEMYLLTGGDRNMYGPTEATMCATW	DAFYLGMMCK	Leu/Leu/Leu	1.00/1.00/1.00	DAFYLGMMCK/DAFYLGMMCK/DAFYLGMMCK	1.00/0.94/0.88	Leu(1.00)	hydrophobic-aliphatic(1.03)	N/A	val,leu,ile,abu,iva(0.21)	leu(0.43)	gly,ala,val,leu,ile,abu,iva(1.00)	val,leu,ile,abu,iva(1.00)

License

NRPS-rs is an open source tool available under the GNU Affero General Public License version 3.0 or greater. See the LICENSE.txt file for details.