def test_determine_qc_protocol_standardPE(self):
"""determine_qc_protocol: standard paired-end run
"""
# Make mock analysis project
p = MockAnalysisProject(
"PJB", ("PJB1_S1_R1_001.fastq.gz", "PJB1_S1_R2_001.fastq.gz",
"PJB2_S2_R1_001.fastq.gz", "PJB2_S2_R2_001.fastq.gz"))
p.create(top_dir=self.wd)
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
self.assertEqual(determine_qc_protocol(project), "standardPE")
def test_determine_qc_protocol_10xchromium3v3(self):
"""determine_qc_protocol: single-cell run (10xGenomics Chromium 3'v3)
"""
# Make mock analysis project
p = MockAnalysisProject(
"PJB", ("PJB1_S1_R1_001.fastq.gz", "PJB1_S1_R2_001.fastq.gz",
"PJB2_S2_R1_001.fastq.gz", "PJB2_S2_R2_001.fastq.gz"),
metadata={'Single cell platform': "10xGenomics Chromium 3'v3"})
p.create(top_dir=self.wd)
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
self.assertEqual(determine_qc_protocol(project), "singlecell")
def test_determine_qc_protocol_10xchromium3v2_atac_seq(self):
"""determine_qc_protocol: single-cell ATAC-seq (10xGenomics Single Cell ATAC)
"""
# Make mock analysis project
p = MockAnalysisProject(
"PJB", ("PJB1_S1_R1_001.fastq.gz", "PJB1_S1_R2_001.fastq.gz",
"PJB2_S2_R1_001.fastq.gz", "PJB2_S2_R2_001.fastq.gz"),
metadata={
'Single cell platform': "10xGenomics Single Cell ATAC",
'Library type': "scATAC-seq"
})
p.create(top_dir=self.wd)
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
self.assertEqual(determine_qc_protocol(project), "10x_scATAC")