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)