def decode(self):
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DECODE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Decode the record's bytes.
[0-3]: SYSTEM TIME
[4-7]: DISPLAY TIME
[8-497]: CONTENT (XML)
[498-499]: CRC
"""
# Initialize decoding
super(XMLRecord, self).decode()
# XML value
self.value = lib.translate(self.bytes[8:-2])
def read(self):
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
READ
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
# Execute command
self.command.execute()
# Assign response
self.id = lib.translate(self.command.response["Payload"])
# Give user info
Logger.info("Transmitter ID: " + str(self.id))
# Store it
self.store()
# 10 = nsp10_CysHis; formerly known as growth-factor-like protein (GFL)
# 11 = only 13 aa
# 12 is mostly and 13-16 in orf1b
# 12 = https://en.wikipedia.org/wiki/RNA-dependent_RNA_polymerase
# 13 = Helicase (Hel).
# 14 = Guanine-N7 methyltransferase (ExoN) or maybe 3'-to-5' exonuclease
# 15 = Uridylate-specific endoribonuclease (NendoU), endoRNAse
# 16 = 2'-O-methyltransferase (2'-O-MT)
# https://en.wikipedia.org/wiki/MRNA_(nucleoside-2%27-O-)-methyltransferase
# in front "the untranslated leader sequence that ends with the Transcription Regulation Sequence"
#Read Mutated sequence from SANTA-SIM
corona[' UNTRANSLATED_REGION '] = cc[0:265]
corona['orf1a'] = translate(cc[266-1:13483], 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
corona['orf1b'] = translate(cc[13468-1:21555], 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/
# 3 = Papain-like proteinase # see diff https://www.ncbi.nlm.nih.gov/projects/msaviewer/?rid=7FXGTZFN016&coloring=cons # 4 = nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab # 5 = Proteinase 3CL-PRO # 6 = ??? # 7 = ??? # 8 = ??? # 9 = ssRNA-binding protein; produced by both pp1a and pp1ab # 10 = nsp10_CysHis; formerly known as growth-factor-like protein (GFL) # 11 is mostly and 12-15 in orf1b # 11 = https://en.wikipedia.org/wiki/RNA-dependent_RNA_polymerase # 12 = Helicase (Hel). # 13 = Guanine-N7 methyltransferase (ExoN) or maybe 3'-to-5' exonuclease # 14 = Uridylate-specific endoribonuclease (NendoU), endoRNAse # 15 = 2'-O-methyltransferase (2'-O-MT), https://en.wikipedia.org/wiki/MRNA_(nucleoside-2%27-O-)-methyltransferase corona['orf1a'] = translate(cc[266-1:13483], True) corona['orf1b'] = translate(cc[13468-1:21555], False) # 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 # sort of 3 proteins, S1 S2 S2' corona['spike_glycoprotein'] = translate(cc[21563-1:25384], True) # Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. corona['orf3a'] = translate(cc[25393-1:26220], True) # these two things stick out corona['envelope_protein'] = translate(cc[26245-1:26472], True) corona['membrane_glycoprotein'] = translate(cc[26523-1:27191], True)
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)
