def test_bam_to_cram(crunchy_config_dict, sbatch_content, bam_path, mocker):
"""Test bam_to_cram method"""
# GIVEN a crunchy-api, and a bam_path
mocker_submit_sbatch = mocker.patch.object(CrunchyAPI, "_submit_sbatch")
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN calling bam_to_cram method on bam-path
crunchy_api.bam_to_cram(bam_path=bam_path, dry_run=False, ntasks=1, mem=2)
# THEN _submit_sbatch method is called with expected sbatch-content
mocker_submit_sbatch.assert_called_with(sbatch_content=sbatch_content,
dry_run=False)
def test_is_bam_compression_possible_cram_done(crunchy_config_dict,
crunchy_test_dir,
mock_bam_to_cram, mocker):
"""Test bam_compression_possible for existing compression"""
# GIVEN a bam path to a existing file and a crunchy api
mocker.patch.object(CrunchyAPI,
"bam_to_cram",
side_effect=mock_bam_to_cram)
crunchy_api = CrunchyAPI(crunchy_config_dict)
bam_path = crunchy_test_dir / "file.bam"
bam_path.touch()
# WHEN calling test_bam_compression_possible when cram_compression is done
crunchy_api.bam_to_cram(bam_path=bam_path, dry_run=False, ntasks=1, mem=2)
result = crunchy_api.is_bam_compression_possible(bam_path=bam_path)
# THEN this should return False
assert not result
def test_cram_compression_before_after(crunchy_config_dict, crunchy_test_dir,
mock_bam_to_cram, mocker):
"""Test cram_compression_done without before and after creating files"""
# GIVEN a crunchy-api, and a bam_path
bam_path = Path(crunchy_test_dir / "file.bam")
mocker.patch.object(CrunchyAPI,
"bam_to_cram",
side_effect=mock_bam_to_cram)
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN calling cram_compression_done on bam_path
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# Cram compression is not done
assert not result
# GIVEN created cram, crai, and flag paths
crunchy_api.bam_to_cram(bam_path=bam_path, dry_run=False, ntasks=1, mem=2)
# WHEN calling cram_compression_done on bam_path
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# THEN compression is marked as done
assert result