diff options
Diffstat (limited to 'tests/unit/test_commands.py')
| -rw-r--r-- | tests/unit/test_commands.py | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py index aafb3a2..f36ba55 100644 --- a/tests/unit/test_commands.py +++ b/tests/unit/test_commands.py @@ -6,6 +6,7 @@ from datetime import datetime from typing import Callable from unittest import mock from gn3.commands import compose_gemma_cmd +from gn3.commands import compose_rqtl_cmd from gn3.commands import queue_cmd from gn3.commands import run_cmd from gn3.exceptions import RedisConnectionError @@ -53,6 +54,30 @@ class TestCommands(unittest.TestCase): "-p /tmp/gf13Ad0tRX/phenofile.txt" " -gk")) + def test_compose_rqtl_cmd(self): + """Test that the R/qtl cmd is composed correctly""" + self.assertEqual( + compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper", + rqtl_wrapper_kwargs={ + "g": "the_genofile", + "p": "the_phenofile", + "model": "np", + "method": "ehk", + "nperm": 2000, + "scale": "Mb", + "control": "rs234567" + }, + rqtl_wrapper_bool_kwargs=[ + "addcovar" + ]), + ("Rscript rqtl-wrapper " + "--g the_genofile --p the_phenofile " + "--model np --method ehk " + "--nperm 2000 --scale Mb " + "--control rs234567 " + "--addcovar") + ) + def test_queue_cmd_exception_raised_when_redis_is_down(self): """Test that the correct error is raised when Redis is unavailable""" self.assertRaises(RedisConnectionError, |