This repository contains the scripts necessary to reproduce the validation of IntFinder (version 1.0).
- Download this repository.
git clone https://github.com/kalilamali/integrons
- Download IntFinder.
git clone https://bitbucket.org/genomicepidemiology/intfinder.git
- Download IntFinder database.
git clone https://bitbucket.org/genomicepidemiology/intfinder_db.git
cd intfinder_db
python3 INSTALL.py
1
cd ..
- Download KMA.
git clone https://bitbucket.org/genomicepidemiology/kma.git
cd kma && make
mv kma /usr/bin/
cd ..
- Your folders and scripts should look like this:
/Integrons
/intfinder
/intfinder_db
/kma
/validation_seqs
CITATION.cff
get_mr0_test_cases.py
get_mr1_test_cases.py
get_mr2_test_cases.py
group_intfinder.py
mrs.py
README.md
- Create the test cases according to the metamorphic relations (MRs).
python3 get_mr0_test_cases.py
python3 get_mr1_test_cases.py
python3 get_mr2_test_cases.py
- Run IntFinder for each test case.
python3 mrs.py
python3 mrs.py > report.tsv
group_intfinder.py uses kma's location:
/usr/bin/kma
if kma is not in that location please update the script.
If you get:
ModuleNotFoundError: No module named 'tabulate'
ModuleNotFoundError: No module named 'cgecore'
It can be fixed with the following comands:
pip3 install tabulate
pip3 install cgecore
Online website: https://cge.food.dtu.dk/services/IntFinder-1.0
IntFinder database expanded to detect integron classes 1, 2, and 3: https://figshare.com/articles/dataset/intfinder_db/14096915