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')
