Kindly if you find this repo useful for your work, cite & star this repo
What is this script?
MicrobeAnnotator is a great tool for metabolic pathway annotation. However, if you need to collect pathway completeness stats from a cohort of genomes into one condensed CSV (to make a heatmap), you are in the right repo!
What do you need?
You shall have the tab files in one directory
What about dependencies?
Pandas, csv, argparse
Then, effortlessly you can type in your beautiful terminal
python3 microanno_stats.py -i ."-i /--input_dir" is your path to the directory for your binary file.
In my case, the script was in the same directory as the Python file. Therefore, I wrote . as my input directory.
What do you get?
Currently, there are two files.
- pathway_group.csv The main output is a collection in the 3rd column which is referred as "pathway_group" in the basic tab output of MicrobeAnnotator.
- detailed_pathway.csv. This is simply a detailed pathway collection in the 2nd column which is referred to as "name" in the basic tab output of MicrobeAnnotator.
You can use the two files in your favorite visualization tool to produce a publication-ready figure.
I hope this helps.
Thanks