Question

Question #2 A DNA molecule can be specified using a string of the characters , ‘g 'a', 't'. Each of these characters represents one of the four nucleobases Cytosine, Guanine, Adenine, and Thymine. Consult the wikipedia page on DNA for more details. A codon consists of a sequence of three DNA nucle- obases and can be represented by a string of length 3 consisting of characters from the set ‘c', ‘g', ‘a", ‘t'. So "cga" and "ttg" are examples of codons and in total there are 64 of them Write a function codon_dict(file_name) that has one string argument, file name, that is the name of a text file whose lines contain a number of codons that are separated by whitespace. The function will return a dictionary whose keys consist of all of the codons that are found in the file and whose values are the number of occurrences of the codon. So, if the codoin "ttg" occurs 5 times in the file, then the value of the returned dictionary for the key "ttg" will be the integer 5. If a particular codon does not appear in the file, then it should not be a key of the dictionary that the function returns In some instances, the upper case l used instead of their lower case counterparts. Your code should not distin guish between upper and lower case letters. So the string "tTG" should be recognized as a valid codon and count as one occurrence of the codon "ttg". etters "C", "G", "A", "T" will be Some strings in the file may have length not equal to three or may con tain other symbols. These strings should be disregarded while producing the dictionary. For example, in the sample file codon file 1.txt found here: https://ms.mcmaster.ca/-matt/1mp3/homework/codon_file_1.txt the strings "123", "$$##0", and "aKg" should not be included in the dictionary.

Answer 1

#codons.py
import itertools,random
#method that generates 64 possible codes for atcg
def get_codons():
   codons = []
   for p in itertools.product('atcg',repeat = 3):
       codons.append("".join(p))
   return codons

#method that returns the count of each valid codon in the given file
def codon_dict(file_name):
   #open file
   inp = open(file_name,"r")
   #split() method without any argument splits the string at white space i.e a space , a tab or a new line
   #to handle uppercase codons , all the text read is converted to lower case
   data = inp.read().strip().lower().split()
   #get codons
   codons = get_codons()
   #create an empty dictionary
   c_dict = {}
   #for each valid codon in generated from get_codons() method
   for code in codons:
       #get the count of the code
       count = data.count(code)
       #if it is > 0
       if(count > 0):
           #create a key in dictionary
           c_dict[code] = count
   #finally return the dictionary
   return c_dict

#call codon_dict()
c_dict = codon_dict("inp.txt")
print("Count of Codons")
for key, value in c_dict.items():
   print(key, value)
#sample input and output screenshot is inserted
#inp.txt

ACT cta AAG CCC AGA CGT ATC GAT CGT GGG TGC
tga TGC CGA TCC ggt tac GGC TGA gtg acc
GTA CAC GGA GGT aga GGT cat tag GGC agc
TTT AAC GCT CTT CAT aga GGC CTC tac tat
GAT tat ata tag gtg AGG aag agg AGG gtt
tcc CGT ccg cca gga TCG aac TGG CTC ATC
CCT TTA CCG TTG TCT TCC ACT TTG TCA aat
TCA AGT TAG tcg TAC CGT CCT AGC TAT CGT
gac cag cag CAT ATC ccg ATA cgg ACA gat
TCC TGA CTT tac TCT aaa agc TTC caa asldj
tc jsdlkj 123 dkdl akd
skdkd djd
djdkjd

ount of Codons C:\Windows SYSTEM32\cmd.exe ag 2 ta 2 tc 3 ct 2 ga 3 gt 1 9g 3 at 3 ag 3 ta 1 tt 1 tc 1 tg 2 ca 2 ct 2 cc 4 cg 2 ga 3 gC 2 99 1 at 3 ag 2 tt 2 ct 2 cg 3 ga 1 gt 5 gg 1 ac 1 ta 1 tt 1 tg 2 ct 1 ga 2 gt 3 Уус 3 gg 1 (program exited with code: ) ss an y key to continue

File Edit earch View Document Project Build Iools Help New Open codons.py X inp.tbtX ave Save All Revert CloseBack Forward Compile BuildExecute Color Chooser ump toQuit 1 ACT cta AAG CCC AGA CGI ATC GAT CGI GGG TGC tga TGC CGA TCC ggt tac GGC TGA gtg acc GTA CAC GGA GGI aga GGI cat tag GGC age III MC GCT CIT CAT aga GGC CTC tac tat GAT tat ata tag gtg AGG aag agg AGG gtt tcc CGI ccg cca gga TCG aac TGG CTC ATC CCT TIA CCG TTG TCT TCC ACT ITG TCA aat TCA AGI TAG teg TAC CGI CCT AGC TAT CGI gac cag cag CAT ATC ccg ATA egg ncn gat TCC TGA CIT tac TCT aaa age TTc caa asld tc Jsdikj 123 dkdl akd gkdkd djd djdkjd 11 13 14 1237 AM