def vimstamp_open_file():
path = vim.bindeval("resolve(expand(\'%\'))").decode("utf-8")
ts = get_time_stamp(path)
s = simplify(vim.current.buffer)
vim.vars["g:vimstamp_idx2stamp"][str(
vim.current.window.buffer.number)] = (s, ts, path)
def vimstamp_write_file():
if str(vim.current.window.buffer.number
) not in vim.vars["g:vimstamp_idx2stamp"]:
return
s, ts, path = vim.vars["g:vimstamp_idx2stamp"][str(
vim.current.window.buffer.number)]
s_new = simplify(vim.current.buffer)
ts_new = get_time_stamp(path)
if s_new == s and ts != ts_new:
set_time_stamp(path, ts)
vim.command("e")
# Not
Not(V("X")) # Negacija spremenljivke.
Not(a1) # Negacija izraza.
print "::: END OPERANDI :::\n\n"
"""
######################################################
#################Simplify#############################
######################################################
"""
from simplify import *
print "::: BEGIN SIMPLIFY :::"
# Nekaj osnovnih primerov uporabe.
print simplify(Not(Not(a2))) # Brise dvojne negacije.
print simplify(Or([V("X"), Not(V("X"))])) # Prepozna tavtologijo.
print simplify(And([V("X"), Not(V("X"))]))
print simplify(And([V("X"), Tru()])) # Pobrise nepotrebne spremenljivke.
print simplify(And([V("X"), V("X"), V("Y")])) # Spremenljivke.
print simplify(And([V("X"), V("X"), V("Y"), Fls()]))
print simplify(Or([Or([V("X"), V("Y")]), Or([V("Y"), V("Z")])]))
print simplify(Not(And([V("X"), V("Y")]))) # Potisnemo negacijo navznoter.
# Razbije izraz na konjunkcije in disjunkcije ter potisne negacijo navznoter.
print simplify(Not(Equiv(V("X"), V("Y"))))
print "::: END SIMPLIFY :::\n\n"
"""
######################################################
#################SAT PREVEDBE#########################
######################################################
flags = {}
for an_id in poly_points.keys():
yr,mn,dy =[ int(i) for i in startdates[an_id].split("-") ]
if yr != 2018:
continue
elif mn < 5:
continue
elif mn == 5 and dy < 25:
continue
elif mn == 8 and dy > 16:
continue
elif mn > 8:
continue
#Simplify geometries
#print(simplify(poly_points[an_id], 0.3, True))
poly_points[an_id] = [[l['x'], l['y']] for l in simplify(poly_points[an_id], 0.01, True)]
for f in data["features"]:
if f["geometry"]["coordinates"] == poly_points[an_id]:
flags[an_id] = True
break
if an_id not in flags.keys():
data["features"].append({"type": "Feature",
"properties": { "id": "null"},
"geometry": { "type": "LineString", "coordinates": poly_points[an_id] }})
with open('strava.geojson', 'w') as fp:
json.dump(data, fp)
# Write out that we have processed this CSV file so that
# on next run, we do not have it repeat process.
f = open(os.path.join(csv_dir, "processed.txt"), 'a')
f.write(a_csv)
def assemble(reads, k, tour_bus_args, low_coverage_cutoff, outfile, write_intermediate): print "construct kmers" kmers = make_kmers(reads, k) print "construct graph" G = construct_de_bruijn_velvet(kmers, "False", '') if write_intermediate: nx.write_gexf(G, 'initial_graph.gexf') print "simplify" simplify(G, False) if write_intermediate: nx.write_gexf(G, 'after_simplify_1.gexf') print "remove tips" remove_tips(G, k) print "simplify" simplify(G, False) if write_intermediate: nx.write_gexf(G, 'after_simplify_2.gexf') print "resolve repeats" resolve_repeats(G) print "tour bus" run_tour_bus(G, tour_bus_args[0],tour_bus_args[1]) if write_intermediate: nx.write_gexf(G, 'after_tour_bus.gexf') print "simplify" simplify(G, False) if write_intermediate: nx.write_gexf(G, 'after_simplify_3.gexf') print 'assemble_paths' assemble_paths(G, 3) if write_intermediate: nx.write_gexf(G, 'after_assemble_paths.gexf') print "remove low coverage nodes" remove_low_coverage(G, low_coverage_cutoff, 2*k) if write_intermediate: nx.write_gexf(G, 'final_graph.gexf') contig_length = [len(a) for a in G.nodes()] mean_contig = float(sum(contig_length)) / len(G.nodes()) ### information about assembly print " " print " *** ASSEMBLY INFORMATION *** " print "number of contigs: " + str(len(G.nodes())) print "contig lengths: " + str(contig_length) print "max contig length: " + str(max(contig_length)) print "mean contig length: " + str(mean_contig) of = open(outfile, 'w') for node in G.nodes(): of.write(node+ '\n') return G.nodes()
def expr_simplify_to_the_same_old(tester, s_expr1, s_expr2): expr1 = string_to_expr.expression_from_string(s_expr1) expr2 = string_to_expr.expression_from_string(s_expr2) expr1 = simplify(expr1, pow_rules.pow_rules+trig_rules.trig_rules, [simplify_expr], m2) expr2 = simplify(expr2, pow_rules.pow_rules+trig_rules.trig_rules, [simplify_expr], m2) tester.assertEqual(expr1, expr2)
from parser import parse
from derive import *
from simplify import *
while 1:
try:
s = raw_input( 'pyderive > ' )
except EOFError:
break
# print( simplify( parse( s ) ) )
print( simplify( derive( parse( s ), 'x' ) ) )
from rules import RULES_CNF, DISTRIB_DNF, DISTRIB_CNF
from simplify import *
from unify import unify_functions
from pprint import pprint
# print(qmc.execute(4, *[0, 3, 5, 6, 7, 9, 12, 13, 15]))
# exit()
# print(simplify(_("TRUE | x")))
# print(simplify(_("((P & Q) & !R) | (P & !(Q | R))")))
# print(find_unifications(_("p(X,Y,Z)"), _("p(Y,Z,X)"), True))
# print([str(apply_subs(x, {
# _("Y"): _("f(a)"),
# _("Z"): _("g(a)"),
# _("X"): _("a")
# })) for x in (_("p(h(Y,Z),f(a),g(a))"), _("p(h(f(X),g(X)),Y,Z)"))])
print(simplify(_("TRUE & x & y")))
#print(simplify(_("P(A) & !P(A) & C")))
#exit()
forms = {
"!!A": "A",
"TRUE & x & y": "x & y",
"P(A) & !P(A) & C": "FALSE",
"TRUE | x": "TRUE",
"FALSE & x": "FALSE",
"!!!!A": "A",
"A & !A": "FALSE",
"A & !B": "A & !B",
"!(a|b)": "!a & !b",
"b & y => y": "TRUE",
"((P & Q) & !R) | (P & !(Q | R))": "P & !R",
"(!Q & !R) | (Q & !R)": "!R",
def assemble(reads, k, tour_bus_args, low_coverage_cutoff, outfile,
write_intermediate):
print "construct kmers"
kmers = make_kmers(reads, k)
print "construct graph"
G = construct_de_bruijn_velvet(kmers, "False", '')
if write_intermediate:
nx.write_gexf(G, 'initial_graph.gexf')
print "simplify"
simplify(G, False)
if write_intermediate:
nx.write_gexf(G, 'after_simplify_1.gexf')
print "remove tips"
remove_tips(G, k)
print "simplify"
simplify(G, False)
if write_intermediate:
nx.write_gexf(G, 'after_simplify_2.gexf')
print "resolve repeats"
resolve_repeats(G)
print "tour bus"
run_tour_bus(G, tour_bus_args[0], tour_bus_args[1])
if write_intermediate:
nx.write_gexf(G, 'after_tour_bus.gexf')
print "simplify"
simplify(G, False)
if write_intermediate:
nx.write_gexf(G, 'after_simplify_3.gexf')
print 'assemble_paths'
assemble_paths(G, 3)
if write_intermediate:
nx.write_gexf(G, 'after_assemble_paths.gexf')
print "remove low coverage nodes"
remove_low_coverage(G, low_coverage_cutoff, 2 * k)
if write_intermediate:
nx.write_gexf(G, 'final_graph.gexf')
contig_length = [len(a) for a in G.nodes()]
mean_contig = float(sum(contig_length)) / len(G.nodes())
### information about assembly
print " "
print " *** ASSEMBLY INFORMATION *** "
print "number of contigs: " + str(len(G.nodes()))
print "contig lengths: " + str(contig_length)
print "max contig length: " + str(max(contig_length))
print "mean contig length: " + str(mean_contig)
of = open(outfile, 'w')
for node in G.nodes():
of.write(node + '\n')
return G.nodes()
