def plotFreq(ciph):
ciph = Format.keepOnly(ciph.lower(), ALPH)
fig, ax = plt.subplots(figsize=(10, 5))
barwidth = 0.3
lettcounts = [FreqAnalysis.englishProbabilities.get(x, 0) for x in ALPH]
ciphprobs = FreqAnalysis.getFrequencies(ciph)
lettplot = []
for x in range(26):
lettplot.append(x - (barwidth / 2))
ax.bar(lettplot, lettcounts, width=barwidth, label="English", color="r")
try:
ciphcounts = [ciphprobs.get(x, 0) / len(ciph) for x in ALPH]
ciphplot = []
for x in range(26):
ciphplot.append(x + (barwidth / 2))
ax.bar(ciphplot, ciphcounts, width=barwidth, label="Cipher Text", color="b")
except ZeroDivisionError:
pass
ax.get_yaxis().set_visible(False)
ax.set_xticks(range(26))
ax.set_xticklabels(ALPH.upper())
ax.legend()
output = io.BytesIO()
FigureCanvas(fig).print_png(output)
return Response(output.getvalue(), mimetype="image/png")
def addSpaces():
if request.method == "POST":
plainText = Format.remove(request.json["plain"], SPACE)
plainText = SpaceAdd.addLongest(plainText)
score = DetectEnglish.detectWord(plainText) * 100
return json.dumps({"plain": plainText, "score": f"{score}% certainty"})
return "error"
def decrypt(ciph):
"""Use a hill-climbing algorithm to decipher a substituted alphabet."""
ciph = Format.keepOnly(ciph.lower(), ALPH)
if not ciph:
return ciph, {x: "" for x in ALPH}
key = [
x[0] for x in FreqAnalysis.getFrequencies(ciph).most_common()
if x[0] in ALPH
]
keyMap = dict(zip(key, letterProbs))
bestKey = []
bestScore = 0
i = 0
while i < 1000:
result = sub(ciph, keyMap)
score = DetectEnglish.detect(result)
if score > bestScore:
bestScore = score
bestKey = list(key)
i = 0
x = random.randint(1, len(key) - 1)
y = random.randint(1, len(key) - 1)
key = list(bestKey)
key[x], key[y] = bestKey[y], bestKey[x]
keyMap = dict(zip(key, letterProbs))
i += 1
bestMap = dict(zip(key, letterProbs))
result = sub(ciph, bestMap)
return result, bestMap
def addForwards(text):
"""Insert spacing into text."""
with open("static/txt/wordlist.txt", encoding="utf-8") as f:
wordset = set(f.read().split("\n"))
string = Format.keepOnly(text, ALPH)
result = []
maxLen = DetectEnglish.getLongest()
x = maxLen
while True:
word = string[:x]
if word in wordset:
result.append(word)
string = string[x::]
x = maxLen
else:
x -= 1
if x == 0 and string:
result.append(string[0])
string = string[1::]
x = maxLen
elif not string:
break
return " ".join(result)
def subInputs():
if request.method == "POST":
changed = request.json["name"][0]
newval = request.json["val"].lower()
if newval == "":
newval = "_"
ciphText = Format.keepOnly(request.json["ciph"].lower(), ALPH)
plainText = Format.remove(request.json["plain"], SPACE).lower()
if plainText == "":
new = ''.join([newval if x in changed else "_" for x in ciphText])
else:
plainText = [x for x in plainText]
for i, letter in enumerate(ciphText):
if letter == changed:
plainText[i] = newval
new = "".join(plainText)
score = DetectEnglish.detectWord(SpaceAdd.add(new)) * 100
return json.dumps({"plain": new, "score": f"{score}% certainty"})
return "error"
def indexOfCoincidence(text):
"""Calculate the Index of Coincidence of a piece of text."""
if len(text) == 1:
return 0
text = Format.keepOnly(text.lower(), ALPH)
count = FreqAnalysis.getFrequencies(text).most_common()
ic = sum([(x[1] * (x[1] - 1)) / (len(text) * (len(text) - 1))
for x in count])
return ic
def chiSquared(text):
"""Calculate the Chi-Squared statistic of a piece of text."""
if not text:
return 0
text = Format.keepOnly(text.lower(), ALPH)
count = {x: text.count(x) for x in letterProbs}
predict = {x[0]: letterProbs.get(x[0], 0) * len(text) for x in count}
return sum([((count[x] - predict[x])**2) / predict[x]
for x in letterProbs])
def decryptWithSubstitution(ciph):
"""Decrypt a general polyalphabetic substitution cipher using mulitple simultaneous hill-climbing algorithms."""
ciph = Format.keepOnly(ciph.lower(), ALPH)
length = len(ciph)
subs = []
for x in range(0, 7):
substring = ciph[x::7]
key = [y[0] for y in FreqAnalysis.getFrequencies(substring).most_common() if y[0] in ALPH]
for char in letterProbs:
if char not in key:
key.append(char)
subs.append((substring, key))
i = 0
bestScore = 0
result = []
for sub in subs:
keyMap = dict(zip(sub[1], letterProbs))
result.append(Substitution.sub(sub[0], keyMap))
result = "".join("".join(b) for b in zip_longest(*result, fillvalue=""))
bestScore = DetectEnglish.detect(result, length=length)
while i < 10000:
x = random.randint(0, len(subs) - 1)
y = random.randint(1, len(subs[x][1]) - 1)
z = random.randint(1, len(subs[x][1]) - 1)
subs[x][1][y], subs[x][1][z] = subs[x][1][z], subs[x][1][y]
result = []
for sub in subs:
keyMap = dict(zip(sub[1], letterProbs))
result.append(Substitution.sub(sub[0], keyMap))
result = "".join("".join(b) for b in zip_longest(*result, fillvalue=""))
score = DetectEnglish.detect(result, length=length)
if score > bestScore:
bestScore = score
i = 0
else:
subs[x][1][y], subs[x][1][z] = subs[x][1][z], subs[x][1][y]
i += 1
result = []
for sub in subs:
keyMap = dict(zip(sub[1], letterProbs))
key = ""
for x in ALPH:
for k, v in keyMap.items():
if k == x:
key += v
result.append(Substitution.sub(sub[0], keyMap))
result = "".join("".join(b) for b in zip_longest(*result, fillvalue=""))
return result
def transposition():
args = {"title": "Transposition", "ciphText": "", "result": "", "score": 0, "keylen": "", "key": ""}
if request.method == "POST":
from Ciphers import Transposition
ciphText = Format.remove(request.form["ciphInput"], PUNC).lower()
keylen = int(request.form["keylenInput"] or 0)
key = request.form["keyInput"]
result, key = Transposition.decrypt(ciphText, key=key, keylen=keylen)
key = ",".join(key)
score = DetectEnglish.detectWord(SpaceAdd.addLongest(result)) * 100
args = {"title": "Transposition", "ciphText": ciphText, "result": result, "score": score, "keylen": keylen, "key": key}
return render_template(f"ciphers/transposition.html", **args)
def substitution():
args = {"title": "Substitution", "ciphText": "", "result": "", "score": 0, "vals": {}}
if request.method == "POST":
from Ciphers import Substitution
ciphText = Format.remove(request.form["ciphInput"], PUNC).lower()
if request.form.get("useSpace"):
result, vals = Substitution.decryptWithSpaces(ciphText)
else:
result, vals = Substitution.decrypt(ciphText)
score = DetectEnglish.detectWord(SpaceAdd.addLongest(result)) * 100
args = {"title": "Substitution", "ciphText": ciphText, "result": result, "score": score, "vals": vals}
return render_template(f"ciphers/substitution.html", **args)
def find(word):
"""Find anagrams of a given word."""
with open("static/txt/wordlist.txt", encoding="utf-8") as f:
wordset = f.read().split("\n")
word = Format.keepOnly(word.lower(), ALPH)
anagrams = []
pattern = sorted(word)
for x in wordset:
if sorted(x) == pattern:
anagrams.append(x)
anagrams.sort()
return anagrams
def decrypt(ciph, keylen=0, key=""):
"""
Attempt decryption of the transposition-enciphered text.
One of keylen or key is required to function.
"""
if not (key or keylen):
return "", ""
ciph = Format.keepOnly(ciph.lower(), ALPH, NUMS)
text = _process(ciph, keylen=keylen, key=key)
if key:
return _decryptWithKey(text, key.split(","))
if keylen < 9:
bestResult, bestKey = _decryptShortKey(text)
else:
bestResult, bestKey = _decryptLongKey(text, keylen)
bestScore = DetectEnglish.detectWord(SpaceAdd.addLongest(bestResult))
text = _process(ciph, keylen=len(ciph) // keylen, key=key)
text = "".join(text)
text = _process(text, keylen=keylen, key=key)
if keylen < 9:
result, key = _decryptShortKey(text)
else:
result, key = _decryptLongKey(text, keylen)
score = DetectEnglish.detectWord(SpaceAdd.addLongest(result))
if score > bestScore:
bestResult = result
bestKey = key
overflow = len(ciph) % keylen
if overflow != 0:
bestScore = 0
lastset = bestResult[-overflow:]
overflow = len(lastset)
for perm in itertools.permutations(lastset, overflow):
result = bestResult[:-overflow] + "".join(perm)
score = DetectEnglish.detectWord(SpaceAdd.addLongest(result))
if score > bestScore:
bestScore = score
bestResult = result
return bestResult, bestKey, bestScore
def addLongest(text):
"""Insert spacing into text. Longest identified words inserted first."""
with open("static/txt/wordlist.txt", encoding="utf-8") as f:
wordset = set(f.read().split("\n"))
string = Format.keepOnly(text, ALPH)
result = [""] * len(string)
maxLen = DetectEnglish.getLongest()
for chunkSize in range(maxLen, 0, -1):
for i in range(0, len(string) - chunkSize + 1):
if string[i:i + chunkSize] in wordset:
result[i] = string[i:i + chunkSize]
string = string.replace(string[i:i + chunkSize],
"." * chunkSize)
result = filter(lambda x: x != "", result)
return " ".join(result)
def decrypt(ciph, key="", keylen=0):
"""Automatically decrypt a vigenere cipher using the Index of Coincidence to find possible key lengths."""
ciph = Format.keepOnly(ciph.lower(), ALPH)
if key:
return decryptWithKey(ciph, key)
if keylen:
return decryptWithKeylen(ciph, int(keylen))
sub = {}
for i in range(2, 26):
sub[i] = []
for j in range(i):
sub[i].append(ciph[j::i])
ic = {}
for i in sub:
avgic = sum(map(DetectEnglish.indexOfCoincidence, sub[i])) / i
if avgic > 0.06:
ic[i] = avgic
bestKey = ""
bestScore = 0
bestResult = ""
for i in ic:
results = []
key = []
for x in sub[i]:
result, shift = Caesar.decrypt(x)
results.append(result)
key.append(shift)
result = Transposition.recreate(results)
score = DetectEnglish.detect(result)
if score > bestScore:
bestScore = score
bestKey = "".join(key)
bestResult = result
return bestResult, ",".join(bestKey), bestScore
else:
FormatClasses(str(filename))
with open(
'../Extrct/%sClassExtraction' %
os.path.basename(sys.argv[1]).rstrip('.txt'), 'rb') as d:
Classifications = joblib.load(d)
if os.path.isfile('../Extrct/%sFeatureExtraction' %
(str(os.path.basename(sys.argv[1]).rstrip('.txt')))):
with open(
'../Extrct/%sFeatureExtraction%s' %
(str(os.path.basename(sys.argv[1]).rstrip('.txt')), int(sys.argv[2])),
'rb') as f:
Features = joblib.load(f)
else:
Format(str(filename), int(sys.argv[2]))
with open(
'../Extrct/%sFeatureExtraction%s' %
(str(os.path.basename(sys.argv[1]).rstrip('.txt')), int(sys.argv[2])),
'rb') as f:
Features = joblib.load(f)
clf = sklearn.tree.DecisionTreeClassifier()
model = clf.fit(Features, Classifications)
with open(
'../Models/%sDTC%s.pkl' %
(os.path.basename(sys.argv[1]).rstrip('.txt'), int(sys.argv[2])),
'wb') as oot:
pickle.dump(model, oot)
def splitKey():
if request.method == "POST":
key = Format.keepOnly(request.json["key"].lower(), ALPH)
key = ",".join([x for x in key])
return json.dumps({"key": key})
return "error"
import re
import os.path
call = time.time()
model = '../Models/globular_signal_peptide_2state.3lineDTC15.pkl'
ws = int(re.findall(r'\d+', model)[2])
with open('../Models/globular_signal_peptide_2state.3lineDTC15.pkl',
"rb") as f:
clf = pickle.load(f)
SpIndexR = {0: 'S', 1: 'G'}
PepstoPred = sys.argv[1]
print("formatting fasta features")
FeaturesPred = Format(PepstoPred, ws)
FeaturesPredOnTest = ParseSeqstoDict(PepstoPred)
print("format complete. Predicting peptides")
prediction = list(clf.predict(FeaturesPred))
#StatsComp = FormatClasses(PepstoPred)
gg = ''
x = 0
FalseS = 0
FalseG = 0
wrong = 0
TotalS = 0
MissedS = 0
#The StatsComp expression was for internal testing - you know the classification of your fasta.
def decryptWithSpaces(ciph, keyMap=""):
"""
Use pattern-matching techniques to decipher a substituted alphabet.
Requires properly spaced ciphertext to be effective.
"""
if not keyMap:
keyMap = {key: set(ALPH) for key in ALPH}
ciph = Format.remove(ciph, PUNC).lower()
if not ciph:
return ciph, {x: "" for x in ALPH}
with open("static/txt/patterns.json", encoding="utf-8") as f:
patterns = json.load(f)
# Reformat text into set
for cw in set(ciph.split(" ")):
newMap = {key: set() for key in ALPH}
# Match pattern to wordlist
pattern = PatternGen.pattern(cw)
if pattern in patterns:
for word in patterns[pattern]:
for i, letter in enumerate(cw):
newMap[letter].add(word[i])
# Remove impossible letters
for letter in set(cw):
keyMap[letter] = keyMap[letter] & newMap[letter] if keyMap[
letter] & newMap[letter] else keyMap[letter]
solved = set()
while True:
# Look for 1-length (solved) mappings
oldSolved = set(solved)
solved = set(
next(iter(val)) for val in keyMap.values() if len(val) == 1)
if oldSolved == solved:
break
# Remove solved letters from other possible mappings
_removeSolved(keyMap, solved)
keyMap = {letter: keyMap[letter] or {"_"} for letter in keyMap}
keylens = {length: [] for length in map(len, keyMap.values())}
for letter in keyMap:
keylens[len(keyMap[letter])].append(letter)
while True:
if len(keylens) == 1:
break
poss = []
for letter in ALPH:
if letter in keylens[1] + keylens[list(keylens)[1]]:
poss.append(keyMap[letter])
else:
poss.append({"_"})
possKeys = list("".join(x) for x in itertools.product(*poss))
_, _, bestMap = getBest(possKeys, ciph)
for k, v in bestMap.items():
if len(v) == 1 and v != "_":
keyMap[k] = {v}
while True:
# Look for 1-length (solved) mappings
oldSolved = set(solved)
solved = set(
next(iter(val)) for val in keyMap.values() if len(val) == 1)
if oldSolved == solved:
break
# Remove solved letters from other possible mappings
_removeSolved(keyMap, solved)
keylens = {length: [] for length in map(len, keyMap.values())}
for letter in keyMap:
keylens[len(keyMap[letter])].append(letter)
return sub(ciph, keyMap), keyMap
