def test_pipeing_simple_process_with_file():
p = gu.run_tools([["cat", "-"], ["wc", "-l"]], input=test_mapping)
lines = 0
while (True):
s = p.stdout.readline()
if s is None or len(s) == 0:
break
lines = int(s.strip())
assert lines == 10
assert p.wait() == 0
def test_pipeing_simple_process_with_file():
p = gu.run_tools([["cat", "-"], ["wc", "-l"]], input=test_mapping)
lines = 0
while(True):
s = p.stdout.readline()
if s is None or len(s) == 0:
break
lines = int(s.strip())
assert lines == 10
assert p.wait() == 0
def test_pipeline_fastaq_input():
ff = gt.InputFile(test_mapping)
p = gu.run_tools([["cat", "-"]], input=ff, force_debug=True)
lines = 0
while (True):
s = p.stdout.readline()
if s is None or len(s) == 0:
break
lines += 1
assert p.wait() == 0
assert lines == 40
def test_pipeline_map_input():
ff = gt.InputFile(test_mapping)
p = gu.run_tools([["cat", "-"]], input=ff, force_debug=True, write_map=True, clean_id=True)
lines = 0
while(True):
s = p.stdout.readline()
if s is None or len(s) == 0:
break
lines += 1
assert p.wait() == 0
assert lines == 10
def test_pipeing_simple_process_with_file_output_file():
(f, out) = tempfile.mkstemp()
os.close(f)
p = gu.run_tools([["cat", "-"], ["wc", "-l"]],
input=test_mapping, output=out)
lines = 0
assert p.wait() == 0
assert os.path.exists(out)
with open(out) as f:
lines = int(f.readline().strip())
assert lines == 10
os.remove(out)
def test_pipeing_simple_process_with_file_output_file():
(f, out) = tempfile.mkstemp()
os.close(f)
p = gu.run_tools([["cat", "-"], ["wc", "-l"]],
input=test_mapping,
output=out)
lines = 0
assert p.wait() == 0
assert os.path.exists(out)
with open(out) as f:
lines = int(f.readline().strip())
assert lines == 10
os.remove(out)