kalilamali / Integrons

Integron analysis tools. Scripts necessary to reproduce the validation of IntFinder (version 1.0).

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