def test_template_attribute_reading_first_mapping():
infile = gt.InputFile(testfiles["test.map"])
for tmpl in infile:
print "Template"
assert tmpl.tag == "HWI-ST661:153:D0FTJACXX:2:1102:13924:124292", tmpl.tag
assert tmpl.blocks == 1, tmpl.blocks
assert tmpl.counters == 3, tmpl.counters
assert tmpl.mcs == 2, tmpl.mcs
assert tmpl.level() == -1, tmpl.level()
break
def test_open_raw_stream_from_stream():
p = subprocess.Popen(["cat", testfiles["bedconvert.map"]],
stdout=subprocess.PIPE)
infile = gt.InputFile(p.stdout)
p.wait()
count = 0
for line in infile.raw_stream():
count += 1
assert line.startswith("WI-ST472_0084:6:1101:1179:2208#CTTGTA")
assert count == 1
def test_open_stream():
p = subprocess.Popen(["cat", testfiles["bedconvert.map"]],
stdout=subprocess.PIPE)
infile = gt.InputFile(p.stdout)
p.wait()
count = 0
for tmpl in infile:
count += 1
assert tmpl.tag == "WI-ST472_0084:6:1101:1179:2208#CTTGTA", tmpl.tag
assert tmpl.blocks == 2, tmpl.blocks
assert count == 1
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_template_unmapped_filter_length():
infile = gt.InputFile(testfiles["test.map.gz"])
assert 1 == len([x for x in gt.unmapped(infile, 1)
]), len([x for x in gt.unmapped(infile, 1)])
assert 5 == len([x for x in gt.unmapped(infile, 0)
]), len([x for x in gt.unmapped(infile, 0)])
assert 1 == len([x for x in gt.unmapped(infile, 2)
]), len([x for x in gt.unmapped(infile, 2)])
assert 0 == len([x for x in gt.unmapped(infile, 3)
]), len([x for x in gt.unmapped(infile, 3)])
assert 0 == len([x for x in gt.unmapped(infile, 4)
]), len([x for x in gt.unmapped(infile, 4)])
def test_template_unique_filter_level():
infile = gt.InputFile(testfiles["test.map.gz"])
assert 1 == len([x for x in gt.unique(infile, 20)
]), "Should be length 1 buyt is: " + str(
[x.level() for x in gt.unique(infile, 20)])
def test_template_uniqness_level():
infile = gt.InputFile(testfiles["test.map"])
levels = [t.level() for t in infile]
assert levels == [-1, 37, 0, -1, 0, 0, 0, 0, 0, 0], levels
def test_iterating_input_file():
infile = gt.InputFile(testfiles["reads_1.fastq"])
count = 0
for line in infile:
count += 1
assert count == 10000, count