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_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_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
def interleave(reads, exclude=-1, threads=1):
return gt.interleave(reads, threads=threads)
