def test_writing_fastq_interleaved(): output = results_dir + "/print_fastq.out" input1 = files.open(testfiles["reads_1.fastq"]) input2 = files.open(testfiles["reads_2.fastq"]) filter.interleave([input1, input2]).write_stream(gt.OutputFile(output), write_map=False) s = 0 with open(output) as f: for l in f: s += 1 assert s == 80000, s
def test_interleaved_pair_aligner_run(): input1 = files.open(testfiles["reads_1.fastq"]) input2 = files.open(testfiles["reads_2.fastq"]) mappings = gem.mapper(filter.interleave([input1, input2]), index) paired = gem.pairalign(mappings, index) assert paired is not None assert sum(1 for x in paired) == 20000 # test dataset does not pair at all
def test_interleaving(): input1 = files.open(testfiles["reads_1.fastq"]) input2 = files.open(testfiles["reads_2.fastq"]) s = 0 for t in filter.interleave([input1, input2]): s += 1 assert s == 20000
def test_interleaved_mapper_run(): input1 = files.open(testfiles["reads_1.fastq"]) input2 = files.open(testfiles["reads_2.fastq"]) mappings = gem.mapper(filter.interleave([input1, input2]), index) assert mappings is not None assert mappings.process is not None assert mappings.filename is None assert sum(1 for x in mappings) == 20000
def test_fastq_filter_interleave(): reads_1 = files.open(testfiles["reads_1.fastq"]) reads_2 = files.open(testfiles["reads_2.fastq"]) num_reads = sum(1 for r in filter.interleave([reads_1, reads_2])) assert num_reads == 20000