transAT_G1000

Analysis of TransAT PKS in the G1000 dataset

Prerequisites

1. Setup BGCFlow following the quickstart guide
2. This analysis utilizes this particular BGCFlow version: dev-0.8.1-2

BGCFLOW_DIR="bgcflow" # change according to your local path of BGCFlow
BGCFLOW_VERSION="dev-0.8.1-2"
(cd $BGCFLOW_DIR && git checkout $BGCFLOW_VERSION)

Usage

1. Clone this repository to your local machine

git clone [email protected]:NBChub/transAT_G1034.git
cd transAT_G1034

2. Create symlinks to existing BGCFlow in your local machine

BGCFLOW_DIR="../bgcflow" # change according to your local path of BGCFlow
ln -s $BGCFLOW_DIR/.snakemake/ .snakemake
ln -s $BGCFLOW_DIR/resources/ resources
ln -s $BGCFLOW_DIR/workflow/ workflow

3. Make sure the input folder are structured correctly. Follow the structure defined in the samples.csv.
4. Run the BGC subworkflow:

conda activate bgcflow
bgcflow run --workflow BGC -c 16 -n # this is a dry-run

5. Remove the -n (dry-run) flag to execute the workflows

Polishing the clinker figures

Due to current issue of clinker: gamcil/clinker#106, the resulting svg from clinker might not be correctly annotated. We provide a script to correct the svg generated using the session json. See notebooks/clinker_svg_correction.py for more details how to use it.