Python interleave Examples

Example #1

File: mapper_tests.py Project: maikroeder/gemtools

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

Example #2

File: mapper_tests.py Project: yesimon/gemtools

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

Example #3

File: mapper_tests.py Project: maikroeder/gemtools

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

Example #4

File: mapper_tests.py Project: maikroeder/gemtools

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

Example #5

File: mapper_tests.py Project: yesimon/gemtools

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

Example #6

File: mapper_tests.py Project: yesimon/gemtools

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

Example #7

File: mapper_tests.py Project: maikroeder/gemtools

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

Example #8

File: mapper_tests.py Project: yesimon/gemtools

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

Example #9

File: files_tests.py Project: yesimon/gemtools

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