Installation

The best way to manage the dependency of this repo is through a conda virtual environment. Use the following commands in your terminal

conda create intactness python=3
conda activate intactness
conda install --file requirements.txt

Please check this site for information.

Running instruction

The whole repo is intended to be used as a template folder for reproducible research purpose. Please create a copy of this folder each time your run the pipeline.

The following steps should be taken in order, in the root folder of the project.

1. Store the DNA sequences in a FASTA file named "seqs.fasta" in data folder
2. Specify your email address on the 5th line in intactness/default.cfg
3. conda activate intactness
4. python3 -m intactness
5. The result is in data/seqs/summary.csv

For advanced users, the settings are stored in intactness/default.cfg.