def test_writing_interleaved_file(): source1 = files.open(testfiles["reads_1.fastq"]) source2 = files.open(testfiles["reads_2.fastq"]) target = results_dir + "/write_interleaved.fastq" out = gt.OutputFile(target) gt.interleave([source1, source2]).write_stream(out, write_map=False) with open(target) as f: lines = f.readlines() assert len(lines) == 80000
def test_iterating_interleaved(): infile_1 = gt.InputFile(testfiles["reads_1.fastq"]) infile_2 = gt.InputFile(testfiles["reads_2.fastq"]) count = 0 for line in gt.interleave([infile_1, infile_2]): count += 1 assert count == 20000, count
def test_template_interleave(): infile1 = gt.InputFile(testfiles["test.map"]) infile2 = gt.InputFile(testfiles["test.map"]) interleave = gt.interleave([infile1, infile2]) levels = [t.level() for t in interleave] assert levels == [ -1, -1, 37, 37, 0, 0, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ], levels
def interleave(reads, exclude=-1, threads=1): return gt.interleave(reads, threads=threads)
def test_template_interleave(): infile1 = gt.InputFile(testfiles["test.map"]) infile2 = gt.InputFile(testfiles["test.map"]) interleave = gt.interleave([infile1, infile2]) levels = [t.level() for t in interleave] assert levels == [-1, -1, 37, 37, 0, 0, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], levels