README.md

Rule based adjectives

The script is currently a blunt implement but there is more in there.

Install

Download the git repo, and change your directory to its root.

git clone https://github.com/rmFlynn/rule_adjectives.git
cd rule_adjectives

Install the conda environment:

conda env create -f environment.yaml
conda activate rule_adjectives # Don't forget this step

Install the packeg:

pip3 install -e ./ # yes you need the -e for now

This is a temporary method of installation while the program is in beta, but a better method will be created after that.

Use

Currently you can annotate genomes and print out cause plots. The options are probably best explained by example.

First use --help to see all options. That will provide context.

rule_adjectives --help

Here is an example that will make a table for all adjectives together:

rule_adjectives ./annotations.tsv ./adjectives.tsv

Here is how you would evaluate just 3 adjective:

rule_adjectives ./annotations.tsv ./adjectives.tsv \
        -a "Autotroph" \
        -a "Heterotroph" \
        -a "sulfatereducer"

Here is how you would evaluate just 3 adjective and plot 2 of them for 2 genomes:

rule_adjectives ./annotations.tsv ./adjectives.tsv \
        -a "Autotroph" \
        -a "Heterotroph" \
        -a "sulfatereducer" \
        --plot_path 'plots_dec1_3' \
        -p "Autotroph" \
        -p "sulfatereducer" \
        -g bin1.scaffold1 \
        -g bin1.scaffold2

Notes

Iron utilizer is not yet fully supported