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")