def test_get_fastq_pairs_single_end(self): s = AnalysisSample("PB1") s.add_fastq("/data/PB/PB1_ATTAGG_L001_R1_001.fastq") s.add_fastq("/data/PB/PB1_GCCAAG_L002_R1_001.fastq") fq_pair = get_fastq_pairs(s) self.assertEqual(len(fq_pair), 2) self.assertEqual(fq_pair[0].r1, "/data/PB/PB1_ATTAGG_L001_R1_001.fastq") self.assertEqual(fq_pair[0].r2, None) self.assertEqual(fq_pair[1].r1, "/data/PB/PB1_GCCAAG_L002_R1_001.fastq") self.assertEqual(fq_pair[1].r2, None)
def test_paired_end(self): s = AnalysisSample('PB1') s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq') s.add_fastq('/data/PB/PB1_ATTAGG_L001_R2_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_R2_001.fastq') self.assertEqual(get_fastq_pairs(s),[('/data/PB/PB1_ATTAGG_L001_R1_001.fastq', '/data/PB/PB1_ATTAGG_L001_R2_001.fastq'), ('/data/PB/PB1_GCCAAG_L002_R1_001.fastq', '/data/PB/PB1_GCCAAG_L002_R2_001.fastq')])
def test_get_fastq_pairs_single_end(self): s = AnalysisSample('PB1') s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq') fq_pair = get_fastq_pairs(s) self.assertEqual(len(fq_pair), 2) self.assertEqual(fq_pair[0].r1, '/data/PB/PB1_ATTAGG_L001_R1_001.fastq') self.assertEqual(fq_pair[0].r2, None) self.assertEqual(fq_pair[1].r1, '/data/PB/PB1_GCCAAG_L002_R1_001.fastq') self.assertEqual(fq_pair[1].r2, None)
def test_get_fastq_pairs_paired_end_with_index_reads(self): s = AnalysisSample('PB1') s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq') s.add_fastq('/data/PB/PB1_ATTAGG_L001_R2_001.fastq') s.add_fastq('/data/PB/PB1_ATTAGG_L001_I1_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_R2_001.fastq') s.add_fastq('/data/PB/PB1_GCCAAG_L002_I1_001.fastq') fq_pair = get_fastq_pairs(s) self.assertEqual(len(fq_pair), 2) self.assertEqual(fq_pair[0].r1, '/data/PB/PB1_ATTAGG_L001_R1_001.fastq') self.assertEqual(fq_pair[0].r2, '/data/PB/PB1_ATTAGG_L001_R2_001.fastq') self.assertEqual(fq_pair[1].r1, '/data/PB/PB1_GCCAAG_L002_R1_001.fastq') self.assertEqual(fq_pair[1].r2, '/data/PB/PB1_GCCAAG_L002_R2_001.fastq')