This repository contains scripts for the analysis of the antigenic structure of bacteria.
You can add add information about operons to the gff file with the help of the merge-operons.py script. The script will add the following qualifiers to the gff file:
- operon: int - operon index
- antigen: [True | False] - whether the gene is an antigen
- antigen_type: [O | H | K] - antigen type
Then draw-operons.py script will draw operons that contain antigen genes with the help of the generated gff file.
python -m pip install -r requirements.txt# get gff with operons-specific features
# the result will be saved in b.gff, b.gff will contain the same features as a.gff,
# but with additional qualifiers for operons and antigen's genes
python merge-operons.py -t O a.gff list_of_operons orfs_coordinates -o b.gff
# You can also search for multiple operons at once
python merge-operons.py -t O -t H -t K a.gff list_of_operons orfs_coordinates -o b.gff
# draw operons
python draw-operons.py b.gff
python oantigen.py -h