Wrong relative path to tests/data/test_isolate_* files

[Peter Cock]

The documentation in the main README file clearly says to run the tests as follows from the main ResFinder directory:

python3 tests/functional_tests.py

However, the code currently refers to test FASTA and FASTQ files via relative paths like data/test_isolate_01.fa - and the tests all fail. Running the individual commands shows error messages about this files not being found (because their path is wrong).

These should all be tests/data/test_isolate_01.fa and so on, or the code could adjust the paths depending where the tests are being run from (e.g. use self.dir_res and os.path.join or similar). Suggested fix:

$ git diff tests/functional_tests.py
diff --git a/tests/functional_tests.py b/tests/functional_tests.py
index 2843f30..12acb42 100755
--- a/tests/functional_tests.py
+++ b/tests/functional_tests.py
@@ -16,11 +16,11 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 test_names = ["test1", "test2", "test3", "test4"]
 test_data = {
     # Test published acquired resistance
-    test_names[0]: "data/test_isolate_01.fa",
-    test_names[1]: "data/test_isolate_01_1.fq data/test_isolate_01_2.fq",
+    test_names[0]: "tests/data/test_isolate_01.fa",
+    test_names[1]: "tests/data/test_isolate_01_1.fq tests/data/test_isolate_01_2.fq",
     # Test published point mut resistance
-    test_names[2]: "data/test_isolate_05.fa",
-    test_names[3]: "data/test_isolate_05_1.fq data/test_isolate_05_2.fq",
+    test_names[2]: "tests/data/test_isolate_05.fa",
+    test_names[3]: "tests/data/test_isolate_05_1.fq tests/data/test_isolate_05_2.fq",
 }
 run_test_dir = "running_test"
 working_dir = os.path.dirname(os.path.realpath(__file__))

‌

‌

[Peter Cock]

Working now, unclear what I did wrong earlier in the week.

Installation on 64-bit Linux with dependencies installed using conda (using conda-forge and bioconda channels):

$ conda install blast kma tabulate biopython cgecore gitpython python-dateutil

Key dependency versions:

$ python3 --version
Python 3.7.9
$ kma -v
KMA-1.3.28
$ blastn -version
blastn: 2.12.0+
 Package: blast 2.12.0, build Jul 13 2021 09:03:00

Using version 4.1.6 from github:

$ git clone https://[e-mail]/genomicepidemiology/resfinder.git
$ cd resfinder
$ git checkout 4.1.6

Databases installed as per https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md documentation,

$ git clone https://[e-mail]/genomicepidemiology/resfinder_db.git db_resfinder
$ cd db_resfinder
$ python3 INSTALL.py
$ cd .. 

and:

$ git clone https://[e-mail]/genomicepidemiology/pointfinder_db.git db_pointfinder
$ cd db_pointfinder
$ python3 INSTALL.py
$ cd ..

Sadly the test suite does not default to blastn and kma being on the path (that might need to change for a conda installation), but we can specify their location:

$ python3 tests/functional_tests.py -b `which blastn` -k `which kma`
....
----------------------------------------------------------------------
Ran 4 tests in 54.526s

OK