def histogram():
args = parse.get_args_ds()
if args == -1:
return
df = parse.read_file(args.fname_dataset)
plot_hist(parse.normalize_df(df))
my_histogram(parse.normalize_df(df))
def main(argv):
arg_parser = argparse.ArgumentParser(prog="blast_sort",
description="A program to look up blast numbers and associated DNA/Protein data from a data file, check it against a list of blasts you want to compare, and save the output of all of the finds in fasta formated files named after the blast number")
arg_parser.add_argument('--blast_file', '-b',
required=True,
help="csv lookup for blast nos")
arg_parser.add_argument('--data_files', '-d', nargs='+',
required=True,
help="data files to search")
arg_parser.add_argument('--output_folder', '-o',
required=True,
help="where to save the results")
arg_parser.add_argument('--verbose', '-v', action='store_true',
required=False,
default=False, help="print status and completion rate")
if len(argv) == 1:
argv.append('--help')
args = arg_parser.parse_args(argv[1:])
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w',0)
output_folder = path(args.output_folder)
# check that the output folder exists
if not output_folder.exists():
output_folder.mkdir()
if not output_folder.isdir():
print "{0} already exists and is not a directory. please choose a directory or a new name"
sys.exit(status=1)
blast_set = read_file(args.blast_file)
for data_file in args.data_files:
check_inclusion(blast_set, data_file, output_folder, args.verbose)
if args.verbose:
print "\n\nDONE! :)"
def main():
args = parse.get_args_ds()
if args == -1:
return
df = parse.read_file(args.fname_dataset)
# Describe
test_describe(df, dc.get_data(df))
def main():
# Read CSV file with pandas
args = parse.get_args_ds()
if args == -1:
return
df = parse.read_file(args.fname_dataset)
# Plot the normalized data for each feature
my_scatter_plot(parse.normalize_df(df.copy()))
def main():
args = parse.get_args_predict()
if args == -1:
exit(1)
df = parse.normalize_df(
parse.read_file(args.fname_dataset, check_hog=False))
df1 = df.copy()[cst.feat_list]
df1 = df1.replace(np.nan, 0.5)
theta = load_thetas(args.fname_weights)
y_pred = lt.predict(theta, df1, df1.shape[0])
print_in_file(y_pred)
def main():
# Read CSV file with pandas
args = parse.get_args_ds()
if args == -1:
return
df = parse.read_file(args.fname_dataset)
# Normalize a copy of the dataframe
df_norm = parse.normalize_df(df.copy())
# Pair plot the normalized grades for each class and each house
my_pair_plot(df_norm, get_classes(df_norm))
def main(): args = parse.get_args_train() if args == -1: return df = parse.normalize_df(parse.read_file(args.fname_dataset)) df1 = df.copy()[['Hogwarts House'] + cst.feat_list] df1 = df1.replace(np.nan, 0.5) rocky = Rocky(df1, tp=(59 if args.accuracy else 100)) rocky.y = rocky.get_binary_house() rocky.gradient() save_thetas(rocky.theta, args.fname_weights) if args.accuracy: accuracy(rocky)
def test_read_file():
filename = './datasets/C50test/AaronPressman/421829newsML.txt'
data = parse.read_file(filename)
assert data[0][:4] == 'U.S.'
def dpll_solve(sudo: Circuit) -> Solution:
return dpll(sudo)
def pycosat_solve(circ: Circuit) -> Solution:
variables = {t.variable for c in circ for t in c}
to_sym = dict(zip(variables, range(1, len(variables) + 1)))
from_sym = {v: k for k, v in to_sym.items()}
sym = []
for c in circ:
sym.append([to_sym[t.variable] if t.sign else -1 * to_sym[t.variable]
for t in c])
sol = next(itersolve(sym), False)
if sol:
return True, {from_sym[abs(s)] : s > 0 for s in sol}
return False, {}
if __name__ == "__main__":
sudo = make_circ(read_file("./circuits/sudoku_circuit.txt"))
sol = pycosat_solve(sudo)
def command_handler(self, command="NA"):
commands = [
"help", "credits", "parse", "viewmem", "viewreg", "start", "next",
"changereg", "changemem", "stop", "exit", "run", "dumpmem"
]
args = command.split(' ')
if args[0] in commands:
if args[0] == "help":
print(
"help\t\t\tView available commands\n" +
"credits\t\t\tView credits\n" +
"parse\t\t\tBegin parsing and syntax checking\n" +
"viewmem\t\t\tExport current memory to a text-file\n" +
"viewreg\t\t\tView the value of a given register\n" +
"start\t\t\tStarts the interpreter\n" +
"next\t\t\tIncrements the interpreter by one instruction\n"
+ "changereg\t\tAlters a given register\n" +
"changemem\t\tAlters a section of memory\n" +
"stop\t\t\tStops the interpreter\n" +
"exit\t\t\tExits the simulator\n" +
"run\t\t\tExecutes the entire assembly file" +
"dumpmem\t\t\tExports the current memory to a txt file")
elif args[0] == "credits":
clear_console()
print("----------Credits----------")
print("Product of Bagel Bois 2019")
print(
"Gary Fishell - Console and Interpreter Architecture Design"
)
print("Salim Aweys - Memory and Register management")
print("Lauren DeLeon - Parser Design and Documentation")
print(
"Kristian Bunda - Memory/Register Design and Assembler Directives management"
)
print(
"SIC and SICXE Instruction implementation - Collective effort"
)
print("---------------------------")
elif args[0] == "parse":
if len(args) != 2:
print("Usage: parse [filename]")
return
while True:
print("SIC (0) or SIC/XE (1)", end=' ')
choice = input()
if (choice == '0'):
self.isExtended = False
break
elif (choice == '1'):
self.isExtended = True
break
else:
print("Invalid choice, try again")
self.instruction_array = (read_file(args[1]))
if self.instruction_array is None:
print("Parsing unsuccesful")
return
self.memory = Memory(self.isExtended)
self.registery = Registery(self.isExtended)
elif args[0] == "viewmem":
if len(args) != 2:
print("Usage: viewmem [address]")
return
if self.memory == None:
print("Please parse a file before viewing memory")
return
address = args[1]
if len(address) == SIZE_OF_BYTE * 2:
memory = self.memory.get_memory(address)
if (memory == None):
print("Address out of bounds or invalid address")
else:
print(memory)
else:
print("Please provide an address in the correct format")
elif args[0] == "viewreg":
if len(args) != 2:
print("Usage: viewreg [register]")
return
if self.registery == None:
print("Please parse a file before viewing registery")
return
reg_choice = args[1]
if self.isExtended and reg_choice in VALID_OPTIONS_EXTENDED:
print(self.registery.get_register(reg_choice))
elif not self.isExtended and reg_choice in VALID_OPTIONS_SIMPLE:
print(self.registery.get_register(reg_choice))
elif args[0] == "start":
self.interpreter = Interpreter(self.instruction_array,
self.memory, self.registery,
self.isExtended)
self.interpreter.assign_address()
elif args[0] == "next":
self.interpreter.execute_next_instruction()
elif args[0] == "run":
while True:
done = self.interpreter.execute_next_instruction()
if done != None:
break
elif args[0] == "dumpmem":
if self.memory == None:
print("Please parse a file before viewing memory")
else:
self.memory.show_mem()
elif args[0] == "changereg":
if len(args) != 3:
print("Usage: changereg [register] [value]")
return
reg_choice = args[1]
value = args[2]
if (len(value) % 2 != 0 or len(value) > 6):
print("Please provide a valid value")
return
if self.isExtended and reg_choice in VALID_OPTIONS_EXTENDED:
print("Adjusting register", reg_choice, "to", value)
elif not self.isExtended and reg_choice in VALID_OPTIONS_SIMPLE:
if self.registery.set_register(reg_choice, value) == False:
print("Invalid value - Setting register failed")
else:
print("Please provide a valid register")
elif args[0] == "changemem":
if len(args) != 3:
print("Usage: changemem [address] [bytevalue]")
return
address = args[1]
value = args[2]
if (len(value) != SIZE_OF_BYTE):
print("Please provide a valid value")
return
if self.memory.set_memory(address, value) == False:
print("Invalid value or address - Setting memory failed")
elif args[0] == "stop":
print("Stopping interpreter")
elif args[0] == "exit":
print("Bye :)")
sys.exit()
else:
print("Invalid command")
