def main():
if len(sys.argv) == 4:
method = int(sys.argv[1])
size = int(sys.argv[2])
repeats = int(sys.argv[3])
else:
print(
"syntax: python3 EvaluateCFRandom.py <method (int)> <size (int)> <repeats (int)>"
)
print("Methods: ")
print("\t0 : dummy")
print("\t1 : Mean Utility")
print("\t2 : Weighted Sum")
print("\t3 : Weighted nNN")
print("\t4 : Average nNN")
return
#all parsing should be done here
path = 'data/jester-data-1.csv'
parsed = parser.Parse(path)
#prep the output files
out = open("out_method_1.csv", "w")
csv_out = csv.writer(out, delimiter=',', quotechar='"')
csv_out.writerow([
'userId', 'itermID', 'Actual_Rating', 'Predicted_Rating',
'Delta_Rating'
])
for _ in range(repeats):
evaluate(parsed, method, size, csv_out)
def fetch_logs():
p = parser.Parse()
files = p.filenames("logs")
logs = []
for f in files:
logs.extend(p.readfile("logs/" + f))
return logs
def simulate_agent(data):
m = parser.Parse(data)
print("Parsed message: {}".format(str(m)))
print("ATK_VEC_{atk_vec} for {duration} seconds".format(**m._asdict()))
for t in m.targets:
print("TARGET: {IP}/{mask}".format(**t._asdict()))
for o in m.options:
print("OPTIONS: {var}={val}".format(**o._asdict()))
def main():
save, read = False, False
if len(sys.argv) == 1:
help()
return
if "--save" in sys.argv:
save = True
if "--read" in sys.argv or "-r" in sys.argv:
read = True
commands = [
"-s", "--search", "--page", "-p", "-c", "--count", "-r", "--read"
]
check()
pars = parser.Parse(commands)
args = pars.parse()
bad = searcher.Search(args, save, read)
bad.search()
def __ProcessReply(self, data):
hex_data = haxorview(data)
self.l.debug("{} bytes recv, hexdump:\n{}".format(len(data), hex_data))
if len(data) < 4:
self.stats['pong'] += 1
else:
self.stats['commands'] += 1
try:
m = parser.Parse(data)
self.l.debug("Parsed message: {}".format(str(m)))
self.l.warn("ATK_VEC_{m.atk_vec} for {m.duration} seconds"\
.format(m=m))
for t in m.targets:
self.l.warn("TARGET: {t.IP}/{t.mask}".format(t=t))
for o in m.options:
self.l.warn("OPTIONS: {o.var}={o.val}".format(o=o))
except:
self.l.error("Unable to parse:\n{}".format(hex_data))
if l == []:
return []
if l[0][0] == lexer.T_NLN:
return eraseFirstNln(l[1:])
else:
return l
ts1 = eraseFirstNln(
list(filter((lambda x: x[0] != lexer.T_PREPROC),
lexer.toTokens(s + '\n'))))
for i in ts1:
print(i)
p1 = parser.fixTree(parser.Parse(ts1))
fout = open('/tmp/graph.dot', 'w')
fout.write('''graph tr {
''')
idx = 0
def drawTree(i, l, rodix):
global idx
thix = 'n' + str(idx)
idx += 1
if type(l) != list:
fout.write(str(thix) + ' [label="' + str(l) + '"];')
fout.write(str(rodix) + ' -- ' + str(thix) + ';')
strx = sys.argv[1]
except:
print "Usage: parser.py filename"
exit(1)
try:
f = open(strx)
except:
print "file '" + strx + "' must be an existing and readble file."
exit(2)
try:
buf = f.read()
except:
print "Cannot read'" + strx + "'"
f.close()
mainview = pangodisp.PangoView()
#mainview.add_text("hello")
xstack = stack.Stack()
lexer.Lexer(buf, xstack, parser.tokens)
#xstack.dump() # To show what the lexer did
parser.Parse(buf, xstack)
# Output results (to show workings)
print _cummulate
main()
else:
print("Please enter the path to the mpileup file\nUsage: python scVILP_main.py -in <path to the mpileup file> -names <path to the list of cell names>")
sys.exit()
if args['missing data threshold']!=None:
missing_data_threshold = float(args['missing data threshold'])
if args['false positive rate']!=None:
fp_given = float(args['false positive rate'])
if args['false negative rate']!=None:
fn_given = float(args['false negative rate'])
if args['maximum number of violations']!=None:
K_ = int(args['maximum number of violations'])
##############################################################################
########################### Parse the mpileup file ###########################
(read_counts, alts, refs, chroms, positions, names, depths) = parser.Parse(cell_names_path, data_path)
n=read_counts.shape[0]
l=read_counts.shape[1]
print("# of taxa: %d" % n)
print("# of mutations: %d" % l)
print("false positive rate given: %f" %fp_given)
print("false negative rate given: %f" %fn_given)
mat_ = optimize(read_count_mat=read_counts,fp=fp_given,fn=fn_given,missing_data_thr=missing_data_threshold, K_vios=K_, mu0=1e-3, mu1=0.5)
#############################################################################
#################### Generate heatmap of the genotypes ######################
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# This program illustrates how a JSOL program can be sent between applications.
# A fib function is created in the first Eval, and then sent to the second Eval
# to be run.
import jsol
import json
import parser
with open('examples/psol/part1.psol') as f:
fib = jsol.Eval(parser.Parse(f.read())).json()
print 'JSOL created!:'
print json.dumps(fib, indent=3)
print 'Passing to other instance...'
with open('examples/psol/part2.psol') as f:
jsol.Eval(parser.Parse(f.read()), argv=fib)