def save_results(matched, notmatched, badquality, skipped, total,
_progress):
total = float(total)
send_message(
save(
"matched",
"{:,} reads ({:.2f} %)".format(matched,
100 * matched / total),
))
send_message(
save(
"notmatched",
"{:,} reads ({:.2f} %)".format(notmatched,
100 * notmatched / total),
))
send_message(
save(
"badquality",
"{:,} reads ({:.2f} %)".format(badquality,
100 * badquality / total),
))
send_message(
save(
"skipped",
"{:,} reads ({:.2f} %)".format(skipped,
100 * skipped / total),
))
send_message(progress(_progress))
def test_string(self):
expected = {
'type': 'COMMAND',
'type_data': 'update_output',
'data': {'bar': 'baz'},
}
self.assertEqual(save('bar', 'baz'), expected)
expected["data"] = {'proc.warning': 'Warning foo'}
self.assertEqual(save('proc.warning', 'Warning foo'), expected)
expected["data"] = {'number': "0"}
self.assertEqual(save('number', '"0"'), expected)
def main():
"""Invoke when run directly as a program."""
args = parse_arguments()
with open(args.input_file) as infile:
data = json.load(infile)
if 'expected_format' in data and 'compatible_fragment_ratio' in data:
print(save('strandedness', data['expected_format']))
print(save('fragment_ratio', str(round(data['compatible_fragment_ratio'], 2))))
else:
print(error("Cannot parse library type information file."))
def main():
"""Invoke when run directly as a program."""
args = parse_arguments()
with open(args.input_file) as infile:
data = json.load(infile)
if "expected_format" in data and "compatible_fragment_ratio" in data:
send_message(save("strandedness", data["expected_format"]))
send_message(
save("fragment_ratio",
str(round(data["compatible_fragment_ratio"], 2))))
else:
send_message(error("Cannot parse library type information file."))
def main():
"""Invoke when run directly as a program."""
args = parse_arguments()
with open(args.input_file) as infile:
data = json.load(infile)
if 'expected_format' in data and 'compatible_fragment_ratio' in data:
print(save('strandedness', data['expected_format']))
print(
save('fragment_ratio',
str(round(data['compatible_fragment_ratio'], 2))))
else:
print(error("Cannot parse library type information file."))
def test_hash(self, copy_mock):
expected = {
'type': 'COMMAND',
'type_data': 'update_output',
'data': {'etc': {'file': 'foo.py'}},
}
self.assertEqual(save('etc', '{"file": "foo.py"}'), expected)
def test_quote(self):
expected = {
'type': 'COMMAND',
'type_data': 'update_output',
'data': {'foo': '"'},
}
self.assertEqual(save('foo', '"'), expected)
def test_number(self):
expected = {'type': 'COMMAND', 'type_data': 'update_output', 'data': {'foo': 0}}
self.assertEqual(save('foo', '0'), expected)
genes[str(x[0])] = x[1:]
return times, genes
if file_name[-4:] == ".xls" or file_name[-5:] == ".xlsx":
times, genes = import_excel(file_name)
else:
times, genes = import_table(file_name)
etcjson = '{"etc":%s}' % json.dumps({
"genes": genes,
"timePoints": times
},
separators=(",", ":"))
send_message(
save(
"etc",
json.dumps({
"genes": genes,
"timePoints": times
},
separators=(",", ":"))))
zipfile = gzip.GzipFile(
filename="",
mode="wb",
fileobj=open("etc.json.gz", "wb"),
mtime=0,
)
zipfile.write(etcjson.encode("utf-8"))
def test_string(self):
self.assertEqual(save('bar', 'baz'), '{"bar": "baz"}')
self.assertEqual(save('proc.warning', 'Warning foo'),
'{"proc.warning": "Warning foo"}')
self.assertEqual(save('number', '"0"'), '{"number": "0"}')
def test_hash(self):
self.assertEqual(save('etc', '{"file": "foo.py"}'),
'{"etc": {"file": "foo.py"}}')
def to_output(self, value):
"""Convert value to process output format."""
return json.loads(resolwe_runtime_utils.save(self.name, value))
def test_number(self):
self.assertEqual(save('foo', '0'), '{"foo": 0}')
def test_number(self):
self.assertEqual(save('foo', '0'), '{"foo": 0}')
def test_quote(self):
self.assertEqual(save('foo', '"'), '{"foo": "\\""}')
def test_quote(self):
self.assertEqual(save('foo', '"'), '{"foo": "\\""}')
def test_hash(self):
self.assertEqual(save('etc', '{"file": "foo.py"}'),
'{"etc": {"file": "foo.py"}}')
def test_string(self):
self.assertEqual(save('bar', 'baz'), '{"bar": "baz"}')
self.assertEqual(save('proc.warning', 'Warning foo'),
'{"proc.warning": "Warning foo"}')
self.assertEqual(save('number', '"0"'), '{"number": "0"}')
def to_output(self, value):
"""Convert value to process output format."""
return json.loads(resolwe_runtime_utils.save(self.name, value))
print('{"rc":"1"}')
exit(1)
def isfloat(value):
"""Check if value is float."""
try:
float(value)
return True
except ValueError:
return False
with utils.gzopen(args.input) as f:
# Split lines by tabs
# Ignore lines without a number in second column
# Build a dictionary of gene-expression pairs
exp = {
"genes": {
gene_exp[0]: float(gene_exp[1])
for gene_exp in (l.split("\t") for l in f)
if len(gene_exp) == 2 and isfloat(gene_exp[1])
}
}
if args.output:
with open(args.output, "w") as f:
json.dump(exp, f)
else:
send_message(save("exp_json", json.dumps(exp, separators=(",", ":"))))