def test_expected_outputs_standardSE(self):
"""
expected_outputs: standard single-end, no strandedness
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", ("PJB1_S1_R1_001.fastq.gz", ),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
# Reference outputs
reference_outputs = (
"PJB1_S1_R1_001_fastqc",
"PJB1_S1_R1_001_fastqc.html",
"PJB1_S1_R1_001_fastqc.zip",
"PJB1_S1_R1_001_model_organisms_screen.png",
"PJB1_S1_R1_001_model_organisms_screen.txt",
"PJB1_S1_R1_001_other_organisms_screen.png",
"PJB1_S1_R1_001_other_organisms_screen.txt",
"PJB1_S1_R1_001_rRNA_screen.png",
"PJB1_S1_R1_001_rRNA_screen.txt",
)
expected = expected_outputs(AnalysisProject(
p.name, os.path.join(self.wd, p.name)),
"qc",
qc_protocol="standardSE")
for e in expected:
self.assertEqual(os.path.dirname(e),
os.path.join(self.wd, p.name, "qc"))
self.assertTrue(os.path.basename(e) in reference_outputs)
for r in reference_outputs:
self.assertTrue(os.path.join(self.wd, p.name, "qc", r) in expected)
def test_expected_outputs_standardPE_with_strand(self):
"""
expected_outputs: standard paired-end with strandedness
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", (
"PJB1_S1_R1_001.fastq.gz",
"PJB1_S1_R2_001.fastq.gz",
),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
# Make mock fastq_strand
mock_fastq_strand_conf = os.path.join(self.wd, p.name,
"fastq_strand.conf")
with open(mock_fastq_strand_conf, 'w') as fp:
fp.write("")
# Reference outputs
reference_outputs = (
"PJB1_S1_R1_001_fastqc",
"PJB1_S1_R1_001_fastqc.html",
"PJB1_S1_R1_001_fastqc.zip",
"PJB1_S1_R1_001_model_organisms_screen.png",
"PJB1_S1_R1_001_model_organisms_screen.txt",
"PJB1_S1_R1_001_other_organisms_screen.png",
"PJB1_S1_R1_001_other_organisms_screen.txt",
"PJB1_S1_R1_001_rRNA_screen.png",
"PJB1_S1_R1_001_rRNA_screen.txt",
"PJB1_S1_R2_001_fastqc",
"PJB1_S1_R2_001_fastqc.html",
"PJB1_S1_R2_001_fastqc.zip",
"PJB1_S1_R2_001_model_organisms_screen.png",
"PJB1_S1_R2_001_model_organisms_screen.txt",
"PJB1_S1_R2_001_other_organisms_screen.png",
"PJB1_S1_R2_001_other_organisms_screen.txt",
"PJB1_S1_R2_001_rRNA_screen.png",
"PJB1_S1_R2_001_rRNA_screen.txt",
"PJB1_S1_R1_001_fastq_strand.txt",
)
expected = expected_outputs(AnalysisProject(
p.name, os.path.join(self.wd, p.name)),
"qc",
fastq_strand_conf=mock_fastq_strand_conf,
qc_protocol="standardPE")
for e in expected:
self.assertEqual(os.path.dirname(e),
os.path.join(self.wd, p.name, "qc"))
self.assertTrue(os.path.basename(e) in reference_outputs)
for r in reference_outputs:
self.assertTrue(os.path.join(self.wd, p.name, "qc", r) in expected)