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_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_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_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