a. Write a function that takes three arguments: an RNA sequence, a codon-aminoacid dictionary, and a point mutation on RNA b. The function should call the function you wrote in Q1c to convert the RNA sequence to amino acid sequence (conversion can run either on the whole sequence or a part of it) c. Then the function should return the index of the aminoacid affected by the mutation and if the mutation changes the amino acid that is coded by the codon (missense mutation or not)
Note: Mutation information should be provided as follows: r.123A>G (on RNA, A in position is 123 is replaced by G) p.Pro252Arg (on protein, proline at position 252 is replaced by arginine)
Q1c codes:
Q1 )
a
f = open("C:/Users/hasan/OneDrive/Masaüstü/for phyton/codon-aa-list.txt") aa_temp = f.readlines()[1:]
aaDict = {} for i in aa_temp: key, value = i.split() aaDict[key] = value print(aaDict)
b
g = open("C:/Users/hasan/OneDrive/Masaüstü/for phyton/seq.txt")
seq = g.read().replace(" ", "").upper() seq = seq.replace("\n", "") seq = ''.join([i for i in seq if not i.isdigit()]) print(seq)
c
amino = "" for i in range(0, len(seq)-(3+len(seq)%3), 3): if aaDict[seq[i:i+3]]== "Stop": continue amino += aaDict[seq[i:i+3]] print ("Protein String: ", amino)
d
with open("C:/Users/hasan/OneDrive/Masaüstü/for phyton/results.txt", "w") as z: z.writelines(amino)
z.close() f.close() g.close()
Note
codon-aa-list
Codon Aminoacid
UUU Phe UUC Phe UUA Leu UUG Leu CUU Leu CUC Leu CUA Leu CUG Leu AUU Ile AUC Ile AUA Ile AUG Met GUU Val GUC Val GUA Val GUG Val UCU Ser UCC Ser UCA Ser UCG Ser CCU Pro CCC Pro CCA Pro CCG Pro ACU Thr ACC Thr ACA Thr ACG Thr GCU Ala GCC Ala GCA Ala GCG Ala UAU Tyr UAC Tyr UAA Stop UAG Stop CAU His CAC His CAA Gln CAG Gln AAU Asn AAC Asn AAA Lys AAG Lys GAU Asp GAC Asp GAA Glu GAG Glu UGU Cys UGC Cys UGA Stop UGG Trp CGU Arg CGC Arg CGA Arg CGG Arg AGU Ser AGC Ser AGA Arg AGG Arg GGU Gly GGC Gly GGA Gly GGG Gly
seq.txt
1 gaguaguccc uucgcaagcc cucauuucac caggcccccg gcuuggggcg ccuuccuucc
61 ccauggcggg acaccuggcu ucggauuucg ccuucucgcc cccuccaggu gguggaggug
121 augggccagg ggggccggag ccgggcuggg uugauccucg gaccuggcua agcuuccaag
181 gcccuccugg agggccagga aucgggccgg ggguugggcc aggcucugag guguggggga
241 uucccccaug ccccccgccg uaugaguucu guggggggau ggcguacugu gggccccagg
301 uuggaguggg gcuagugccc caaggcggcu uggagaccuc ucagccugag ggcgaagcag
361 gagucggggu ggagagcaac uccgaugggg ccuccccgga gcccugcacc gucaccccug
421 gugccgugaa gcuggagaag gagaagcugg agcaaaaccc ggaggagucc caggacauca
481 aagcucugca gaaagaacuc gagcaauuug ccaagcuccu gaagcagaag aggaucaccc
541 ugggauauac acaggccgau guggggcuca cccugggggu ucuauuuggg aagguauuca
601 gccaaacgac caucugccgc uuugaggcuc ugcagcuuag cuucaagaac auguguaagc
661 ugcggcccuu gcugcagaag uggguggagg aagcugacaa caaugaaaau cuucaggaga
721 uaugcaaagc agaaacccuc gugcaggccc gaaagagaaa gcgaaccagu aucgagaacc
781 gagugagagg caaccuggag aauuuguucc ugcagugccc gaaacccaca cugcagcaga
841 ucagccacau cgcccagcag cuugggcucg agaaggaugu gguccgagug ugguucugua
901 accggcgcca gaagggcaag cgaucaagca gcgacuaugc acaacgagag gauuuugagg
961 cugcuggguc uccuuucuca gggggaccag uguccuuucc ucuggcccca gggccccauu
1021 uugguacccc aggcuauggg agcccucacu ucacugcacu guacuccucg gucccuuucc
1081 cugaggggga agccuuuccc ccugucuccg ucaccacucu gggcucuccc augcauucaa
1141 acugaggugc cugcccuucu aggaaugggg gacaggggga ggggaggagc uagggaaaga
1201 aaaccuggag uuugugccag gguuuuuggg auuaaguucu ucauucacua aggaaggaau
1261 ugggaacaca aagggugggg gcaggggagu uuggggcaac ugguuggagg gaaggugaag
1321 uucaaugaug cucuugauuu uaaucccaca ucauguauca cuuuuuucuu aaauaaagaa
1381 gccugggaca caguagauag acacacuua
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