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Adds a user interface on the console #66

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ed441c6
Implemented a facade pattern to opt.py
Lajellu Apr 9, 2021
f6c0814
Applied creation pattern to corona class
Lajellu Apr 9, 2021
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134 changes: 119 additions & 15 deletions opt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,23 +2,127 @@
from lib import cc as virus
from vaccine.load import dat as vaccine
from corona import corona
from viralDNA import viralDNA

virus = virus.replace("T", "U")
vaccine = vaccine.replace("Ψ", "U")
print("\n\nWelcome to: Reverse engineering the coronavirus\n---------------------------")

"""
for i in range(len(virus)-len(vaccine)):
mm = virus[i:i+len(vaccine)]
mr = sum([c1 == c2 for c1,c2 in zip(mm, vaccine)]) / len(vaccine)
if mr > 0.5:
print(i, mr)
exit(0)
"""
# Allows a maximum of 25 gene snippit lengths to be provided
# These are later passed to the virualDNA prototype
vaccine_i = 21562

# vaccine starts at 21508 with a 67% match
# spike protein starts at 21562
vvirus = virus[21508:21508+len(vaccine)]
regions = {
"untranslated_region_f" : 265,
"orf1a_i" : 266 ,
"orf1a_f" : 13483,
"orf1b_i" : 13468,
"orf1b_f" : 21555,
"spike_gp_i" : 21563,
"spike_gp_f" : 25384,
"orf3a_i" : 25393,
"orf3a_f" : 26220,
"envelope_p_i" : 26245,
"envelope_p_f" : 26472,
"membrane_gp_i" : 26523,
"membrane_gp_f" : 27191,
"orf6_i" : 27202,
"orf6_f" : 27387,
"orf7a_i" : 27394,
"orf7a_f" : 27759,
"orf7b_i" : 27756,
"orf7b_f": 27887,
"orf8_i" : 27894,
"orf8_f" : 28259,
"n_p_i" : 28274,
"n_p_f" : 29533,
"orf10_i" : 29558,
"orf10_f" : 29674,
"new_region_i" : 0,
"new_region_f" : 0}

# User has 10 chances to change the regions
for i in range(10):
print("1 - Add a new gene region\n2 - Change a gene region value\n3 - Add the vaccine start index\n4 - Translate/GO")

# User wants to add a new gene region
user_action = int(input())
if (user_action == 1):
print("Press 0 to stop. Enter the start index of the new region: ?")
new_region_i = int(input())

if (new_region_i != 0):
print("Press 0 to stop. Enter the final index of the new region: ?")
new_region_f = int(input())

elif (user_action == 2):
# for region in region_names:
print("Which region do you want to change?\n")
print("Type 0 to go back to Main Menu. Type -1 to skip. Choose a menu option:")
print("1 - Start position of orf1a (Default = 266)\n")
print("2 - End position of orf1a (Default = 13483)\n")
print("3 - Start position of orf1b (Default = 13468)\n")
print("4 - End position of orf1b (Default = 21555)\n")
print("5 - Start position of spike glycoprotein (Default = 21563)\n")
print("6 - End position of spike glycoprotein (Default = 25384)\n")
print("7 - Start position of orf3a (Default = 25393)\n")
print("8 - End position of orf3a (Default = 26220)\n")
print("9 - Start position of envelope protein (Default = 26245)\n")
print("10 - End position of envelope protein (Default = 26472)\n")
print("11 - Start position of membrane glycoprotein (Default = 26523)\n")
print("12 - End position of membrane glycoprotein (Default = 27191)\n")
print("13 - Start position of orf6 (Default = 27202)\n")
print("14 - End position of orf6 (Default = 27387)\n")
print("15 - Start position of orf7a (Default = 27394)\n")
print("16 - End position of orf7a (Default = 27759)\n")
print("17 - Start position of orf7b (Default = 27756)\n")
print("18 - End position of orf7b (Default = 27887)\n")
print("19 - Start position of orf8 (Default = 27894)\n")
print("20 - End position of orf8 (Default = 28259)\n")
print("21 - Start position of nucleocapsid phosphoprotein (Default = 28274)\n")
print("22 - End position of nucleocapsid phosphoprotein (Default = 29533)\n")
print("23 - Start position of orf10 (Default = 29558)\n")
print("24 - End position of orf10 (Default = 29674)\n")
print("25 - Start position of vaccine (Default = 21508)\n")

region_to_change = int(input())

print("\nWhat is the new position?: \n")


try:
new_position = int(input())
regions[region_to_change] = new_position
print("\nChanged value:\n ------------\n " + str(regions[region_to_change]) + "\n")
except:
print("You must enter an integer value.")


elif (user_action == 3):
print("Start (index) of the vaccine: ?")
vaccine_i = int(input())

elif (user_action == 4):
viralDNA = viralDNA(regions)
virus = virus.replace("T", "U")
vaccine = vaccine.replace("Ψ", "U")

"""
for i in range(len(virus)-len(vaccine)):
mm = virus[i:i+len(vaccine)]
mr = sum([c1 == c2 for c1,c2 in zip(mm, vaccine)]) / len(vaccine)
if mr > 0.5:
print(i, mr)
exit(0)
"""

# vaccine starts at 21508 with a 67% match
# spike protein starts at 21562
vvirus = virus[vaccine_i:vaccine_i+len(vaccine)]

print("\n Vaccine in the Virus Gene Seqence \n ------------------------ \n")
print(vvirus)

print("\n Vaccine Gene Seqence \n ------------------------ \n")
print(vaccine)
#viralDNA = viralDNA(untranslated_region_f = untranslated_region_f, orf1a_i = orf1a_i, orf1a_f = orf1a_f, orf1b_i = orf1b_i,orf1b_f = orf1b_f, spike_gp_i = spike_gp_i, spike_gp_f = spike_gp_f, orf3a_i = orf3a_i, orf3a_f = orf3a_f, envelope_p_i = envelope_p_i, envelope_p_f = envelope_p_f, membrane_gp_i = membrane_gp_i, membrane_gp_f = membrane_gp_f, orf6_i = orf6_i, orf6_f = orf6_f, orf7a_i = orf7a_i, orf7a_f = orf7a_f, orf7b_i = orf7b_i, orf7b_f = orf7b_f, orf8_i = orf8_i, orf8_f = orf8_f, n_p_i = n_p_i, n_p_f = n_p_f, orf10_i = orf10_i, orf10_f = orf10_f, new_region_i = 0, new_region_f = 10)

print(vvirus)
print(vaccine)

167 changes: 167 additions & 0 deletions viralDNA.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,167 @@
from lib import cc, translate
import copy

class viralDNA:
# Defaults are set for corona virus
def __init__(self, regions):

untranslated_region_f = regions["untranslated_region_f"]
orf1a_i = regions["orf1a_i"]
orf1a_f = regions["orf1a_f"]
orf1b_i = regions["orf1b_i"]
orf1b_f = regions["orf1b_f"]
spike_gp_i = regions["spike_gp_i"]
spike_gp_f = regions["spike_gp_f"]
orf3a_i = regions["orf3a_i"]
orf3a_f = regions["orf3a_f"]
envelope_p_i = regions["envelope_p_i"]
envelope_p_f = regions["envelope_p_f"]
membrane_gp_i = regions["membrane_gp_i"]
membrane_gp_f = regions["membrane_gp_f"]
orf6_i = regions["orf6_i"]
orf6_f = regions["orf6_f"]
orf7a_i = regions["orf7a_i"]
orf7a_f = regions["orf7a_f"]
orf7b_i = regions["orf7b_i"]
orf7b_f = regions["orf7b_f"]
orf8_i = regions["orf8_i"]
orf8_f = regions["orf8_f"]
n_p_i = regions["n_p_i"]
n_p_f = regions["n_p_f"]
orf10_i = regions["orf10_i"]
orf10_f = regions["orf10_f"]
new_region_i = regions["new_region_i"]
new_region_f = regions["new_region_f"]

print("Initializing Custom viral DNA\n")

# in front "the untranslated leader sequence that ends with the Transcription Regulation Sequence"
self.untranslated_region = cc[0 : untranslated_region_f]

print("Translatng orf1a ... \n")
self.orf1a = translate(cc[orf1a_i - 1 : orf1a_f], True)

# cc[266-1+4398*3:13468] = 'TTT_TTA_AAC' aka 'X_XXY_YYZ'
# https://en.wikipedia.org/wiki/Ribosomal_frameshift
# Programmed −1 Ribosomal Frameshifting
# TODO: add this to the translate function with automatic detection
print("Translatng orf1b ... \n")
self.orf1b = translate(cc[orf1b_i - 1 : orf1b_f], False).strip("*") # chop off the stop, note this doesn't have a start

# exploit vector, this attaches to ACE2. also called "surface glycoprotein"
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VYB -- open state
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VXX -- closed state
# 1273 amino acids
# S1 = 14-685
# S2 = 686-1273
# S2' = 816-1273
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750777/
print("Translatng spike glycoprotein ... \n")
self.spike_glycoprotein = translate(cc[spike_gp_i - 1 :spike_gp_f], True)

print("Translatng orf3 ... \n")
# Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release.
self.orf3a = translate(cc[orf3a_i-1:orf3a_f], True)

print("Translatng envelope protein ... \n")
# These two characteristics stick out, used in assembly aka they package the virus
self.envelope_protein = translate(cc[envelope_p_i - 1 : envelope_p_f], True) # also known as small membrane

print("Translatng membrane glycoprotein ... \n")
print("membrane_gp_i : " + str(membrane_gp_i))
print("membrane_gp_f : " + str(membrane_gp_f))
self.membrane_glycoprotein = translate(cc[membrane_gp_i - 1 : membrane_gp_f], True)

print("Translatng orf6 ... \n")
self.orf6 = translate(cc[orf6_i - 1 : orf6_f], True)

print("Translatng orf7a ... \n")
self.orf7a = translate(cc[orf7a_i - 1 : orf7a_f], True)

print("Translatng orf7b ... \n")
self.orf7b = translate(cc[orf7b_i - 1 : orf7b_f], True) # is this one real?

print("Translatng orf8 ... \n")
self.orf8 = translate(cc[orf8_i - 1 : orf8_f], True)

# https://en.wikipedia.org/wiki/Capsid
# Packages the positive strand viral genome RNA into a helical ribonucleocapsid
# Includes the "internal" protein (from Coronavirus Pathogenesis)
# https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/human-coronavirus-oc43
print("Translatng nucleocapsid phosphoprotein ... \n")
self.nucleocapsid_phosphoprotein = translate(cc[n_p_i - 1 : n_p_f], True)

print("Translatng orf10 ... \n")
# might be called the internal protein (Coronavirus Pathogenesis)
self.orf10 = translate(cc[orf10_i - 1 : orf10_f], True)



def __copy__(self):
"""
Shallow copy.
Call with copy.copy
Return value of copy.copy is new shallow copy
"""

# Copies of the class fields (nested objects)
untranslated_region = copy.copy(self.untranslated_region)
orf1a = copy.copy(self.orf1a)
orf1b = copy.copy(self.orf1b)
spike_glycoprotein = copy.copy(self.spike_glycoprotein)
orf3a = copy.copy(self.orf3a)
envelope_protein = copy.copy(self.envelope_protein)
membrane_glycoprotein = copy.copy(self.membrane_glycoprotein)
orf6 = copy.copy(self.orf6)
orf7a = copy.copy(self.orf7a)
orf7b = copy.copy(self.orf7b)
orf8 = copy.copy(self.orf8)
nucleocapsid_phosphoprotein = copy.copy(self.nucleocapsid_phosphoprotein)
orf10 = copy.copy(self.orf10)

new = self.__class__(
self.some_int, some_list_of_objects, some_circular_ref
)
new.__dict__.update(self.__dict__)

return new

def __deepcopy__(self, memo={}):
"""
Deep copy
Call with copy.deepcopy
Return value of copy.deepcopy is new deep copy
Memo is the dictionary used by the `deepcopy` library - prevents circular references.
"""
# Copies of the class fields (nested objects)
untranslated_region = copy.deepcopy(self.untranslated_region, memo)
orf1a = copy.deepcopy(self.orf1a, memo)
orf1b = copy.deepcopy(self.orf1b, memo)
spike_glycoprotein = copy.deepcopy(self.spike_glycoprotein, memo)
orf3a = copy.deepcopy(self.orf3a, memo)
envelope_protein = copy.deepcopy(self.envelope_protein, memo)
membrane_glycoprotein = copy.deepcopy(self.membrane_glycoprotein, memo)
orf6 = copy.deepcopy(self.orf6, memo)
orf7a = copy.deepcopy(self.orf7a, memo)
orf7b = copy.deepcopy(self.orf7b, memo)
orf8 = copy.deepcopy(self.orf8, memo)
nucleocapsid_phosphoprotein = copy.deepcopy(self.nucleocapsid_phosphoprotein, memo)
orf10 = copy.deepcopy(self.orf10, memo)

# Then, let's clone the object itself, using the prepared clones of the
# nested objects.
new = self.__class__(
self.untranslated_region, orf1a, orf1b, spike_glycoprotein, orf3a, envelope_protein, membrane_glycoprotein, orf6, orf7a, orf7b, orf8, nucleocapsid_phosphoprotein, orf10
)
new.__dict__ = copy.deepcopy(self.__dict__, memo)

return new


if __name__ == "__main__":
custom_viralDNA = viralDNA()

shallow_copied_viralDNA = copy.copy(custom_viralDNA)
deep_copied_viralDNA = copy.deepcopy(custom_viralDNA)