def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data",
"automated")
self.config_file = os.path.join(self.data_dir,
get_post_process_yaml(self))
assert os.path.exists(
self.config_file
), "Could not locate required configuration file %s" % self.config_file
def test_5_bam(self):
"""Allow BAM files as input to pipeline.
"""
self._install_test_files(self.data_dir)
with make_workdir():
cl = ["automated_initial_analysis.py",
get_post_process_yaml(self),
os.path.join(self.data_dir, os.pardir, "100326_FC6107FAAXX"),
os.path.join(self.data_dir, "run_info-bam.yaml")]
subprocess.check_call(cl)
def test_2_rnaseq(self):
"""Run an RNA-seq analysis with TopHat and Cufflinks.
"""
self.setUp()
self._install_test_files(self.data_dir)
with make_workdir():
cl = ["automated_initial_analysis.py",
get_post_process_yaml(self),
os.path.join(self.data_dir, os.pardir, "110907_ERP000591"),
os.path.join(self.data_dir, "run_info-rnaseq.yaml")]
subprocess.check_call(cl)
def test_4_empty_fastq(self):
"""Handle analysis of empty fastq inputs from failed runs.
"""
self.setUp()
self._install_test_files(self.data_dir)
with make_workdir():
cl = ["automated_initial_analysis.py",
get_post_process_yaml(self),
os.path.join(self.data_dir, os.pardir, "110221_empty_FC12345AAXX"),
os.path.join(self.data_dir, "run_info-empty.yaml")]
subprocess.check_call(cl)
def test_3_full_pipeline(self):
"""Run full automated analysis pipeline with multiplexing.
"""
self.setUp()
self._install_test_files(self.data_dir)
with make_workdir():
cl = ["automated_initial_analysis.py",
get_post_process_yaml(self),
os.path.join(self.data_dir, os.pardir, "110106_FC70BUKAAXX"),
os.path.join(self.data_dir, "run_info.yaml")]
subprocess.check_call(cl)
def test_1_variantcall(self):
"""Test variant calling with GATK pipeline.
"""
self.setUp()
self._install_test_files(self.data_dir)
with make_workdir():
cl = ["automated_initial_analysis.py",
get_post_process_yaml(self),
os.path.join(self.data_dir, os.pardir, "100326_FC6107FAAXX"),
os.path.join(self.data_dir, "run_info-variantcall.yaml")]
subprocess.check_call(cl)
def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data", "automated")
self.config_file = os.path.join(self.data_dir, get_post_process_yaml(self))
assert os.path.exists(self.config_file), "Could not locate required configuration file %s" % self.config_file