processAntiSmash: summarise antiSMASH 5.0 KnownClusterBlast output

Nick Crosbie, October 2019

Summarises antiSMASH 5.0 (Blin et al. 2019) KnownClusterBlast output (individual pairings) for Biosynthetic Gene Clusters at a user-specified threshold for percent identity and percent coverage. The output is combined with metadata from MIBiG JSON files and written to a single TSV file.

License: GPL-3.0

Dependencies: GNU bash (recent version with readarray), gawk, jq

Input requirements: antiSMASH 5.0 output JSON file(s); Version 2.0 MIBiG data files in JSON format

Example data: three antiSMASH 5.0 output JSON files are included in the ./processAntiSmash/exampleData directory

Example output: an example output TSV file (clustersOutExample.tsv) is included in the ./processAntiSmash/exampleOutput directory

Limitation: To keep the number of columns in the output manageable, only three product compounds are written to clustersOut.tsv

Note: antiSMASH 5.0 uses the DIAMOND software to produce blast-like output and 'blastscore' and 'evalue' are used in that context

1. INSTALL THE SOFTWARE

processAntiSmash and its dependencies can be installed (i) as a docker image, or (ii) by cloning the github repository and separately installing all dependencies. The former approach is easier as it requires fewer steps, less experience with the UNIX command line, and furthermore you can't accidentally clobber your favourite shell environment.

(i) Install as a docker image (Mac or Debian/Ubuntu linux)

1. Install Docker CE or Docker Desktop by following instructions at https://docs.docker.com/install/
2. Start the Docker application
3. Make a directory called as-files
4. If on a Mac, then configure the shared paths from Docker Desktop at Preferences... -> File Sharing. Set path-to/as-files (you'll need to replace the path-to part)
5. Download the processAntiSmash docker image

docker pull milesforjazz/process-antismash

This will install the docker image milesforjazz/process-antismash on your system, which you can verify by issuing the following command

docker images

(ii) Install by cloning from GitHub and separately installing the dependencies

On Debian/Ubuntu linux

1. Install the dependencies

sudo apt-get update; sudo apt-get install git bash coreutils gawk jq

2. Clone the processAntiSmash repository by issuing the following command

git clone https://github.com/crosbien/processAntiSmash.git

On Mac

1. Install Homebrew by issuing the following command

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install the dependencies by issuing the following command

brew update; brew install git; brew install bash; brew install coreutils; brew install gawk; brew install jq

3. Clone the processAntiSmash repository by issuing the following command

git clone https://github.com/crosbien/processAntiSmash.git

2. SETUP WORKING DIRECTORIES AND DOWNLOAD MIBiG FILES

(i) Setup the following working directories:

as-files/data (where you'll put your antiSMASH 5.0 output JSON files)

as-files/out (where the TSV output file will be written)

(ii) Copy your antiSMASH output JSON files to the as-files/data directory

(iii) Download and unpack MIBiG JSON files

1. Issue the following command from the as-files directory to download the MIBiG JSON archive, unpack the files and rename the mibig_json_2.0 directory to mibig

curl https://dl.secondarymetabolites.org/mibig/mibig_json_2.0.tar.gz | tar xvz; mv mibig_json_2.0 mibig 

3. USAGE

(i) Run as a docker container from the command line (if you have installed the docker image)

1. Export variables to the shell by issuing the following from the command line, adjusting the PERC_ID (percent identity) and PERC_COV (percent coverage) values according to need (here both have been set to a value of 70)

export PERC_ID=70 && export PERC_COV=70 && export DATADIR=./datavol/data && export RESULTDIR=./datavol/out && export MIBIG=./datavol/mibig

2. Run the processAntiSmash program as a docker container by issuing the following from the command line (you will need to change the path-to part of the following command to reflect where you have put your as-files directory)

docker run -e PERC_ID -e PERC_COV -e DATADIR -e RESULTDIR -e MIBIG --name processAntiSmash --rm -v /path-to/as-files:/datavol milesforjazz/process-antismash

The output data file will be written to ./path-to/as-files/out clustersOut.tsv

A list of processed data files will be written to ./path-to/as-files/out processed-data-files.tsv

(ii) Run natively by issuing the following commands:

(if you have cloned the github repository and installed all dependencies)

1. Export variables to the shell by issuing the following from the command line, adjusting the PERC_ID (percent identity) and PERC_COV (percent coverage) values according to need (here both have been set to a value of 70). You will need to change the path-to part of the following command to reflect where you have put your as-files directory.

export PERC_ID=70 && export PERC_COV=70 && export DATADIR=/path-to/as-files/data && export RESULTDIR=/path-to/as-files/out && export MIBIG=/path-to/as-files/mibig

2. Execute the bash script

./mibig.sh

(you may need to alter the path to mibig.sh)

The output data file will be written to ./path-to/as-files/out clustersOut.tsv

A list of processed data files will be written to ./path-to/as-files/out processed-data-files.tsv

4. CITATION

Crosbie ND (2019) processAntiSmash: a tool to summarise antiSMASH 5.0 KnownClusterBlast output. https://github.com/crosbien/processAntiSmash

5. REFERENCE

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Yup Lee S, Medema MH, Weber T (2019) antiSMASH 5.0 updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research 47(W1):W81-W87. https://doi.org/10.1093/nar/gkz310