IntFinder development and validation

This repository contains the scripts necessary to reproduce the validation of IntFinder (version 1.0).

1. Download this repository.

git clone https://github.com/kalilamali/integrons

2. Download IntFinder.

git clone https://bitbucket.org/genomicepidemiology/intfinder.git

3. Download IntFinder database.

git clone https://bitbucket.org/genomicepidemiology/intfinder_db.git
cd intfinder_db
python3 INSTALL.py
1
cd ..

4. Download KMA.

git clone https://bitbucket.org/genomicepidemiology/kma.git
cd kma && make
mv kma /usr/bin/
cd ..

5. 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

6. 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

7. Run IntFinder for each test case.

python3 mrs.py
python3 mrs.py > report.tsv

FAQ:

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

Notes:

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