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List/String seperation issue
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List/String seperation issue
#7
   
(Sep-20-2019, 06:33 AM)perfringo Wrote:
(Sep-19-2019, 01:56 PM)YoungGrassHopper Wrote: DD is not a full codon and needs to be removed from the sequence

This code will not work according to requirement set above. You should add check about length:

chunks = [dna[y-x:y] 
          for y in range(x, len(dna)+x, x) 
          if len(dna[y-x:y]) == 3]  


Hi perfringo, yes sorry I did not include that part on the post, that part is sorted though. I am struggling with getting the chunks joined in list form after they get divided in workable chunks of [['A','A','A'],['B','B','B'],['C','C','C']]

I need to get them like this : [['AAA'],['BBB'],['CCC']]
I tried ''.join(chunks) but to luck

And Then I have a for loop issue. Basically I want to have the loop run through these chucks above and check if they match any of the Amino acids I am checking for. My whole approach can be wrong, I realise that. Basically I need to work it all into a function. the argument that gets passed through the function is the dna sequence of arbitrary length, the return needs to be which amino acids the codons (AAA) ; BBB represents, My code below has the actual codons in it so it might look confusing, but I attach pic of the amino acids I need to cover. Mayb if you feel like helping out a youngGrassHopper can tell me where I am going wrong with this?


dna = input("Enter DNA sequence: ")
dna = list(dna)
DNA = len(dna)

if (DNA % 3 == 1 ): 
    del dna[-1]
    
elif (DNA % 3 == 2):
    del dna[-2::]

print(dna)
    
C=3 
chunks = [dna[y-C:y] for y in range(C, len(dna)+C,C)]
                                                         
print(chunks)                        

Isoleucine = 0
Leucine = 0
Valine = 0
Phenylalanine = 0
Methionine = 0    
                    
for i in chunks:                                                    
    if (i == "ATT")or(i == "ATC")or(i == "ATA"):
        Isoleucine += 1

    elif (i == "CTT")or(i == "CTC")or(i == "CTA")or(i == "CTG")or(i == "TTA")or(i == "TTG"):
        Leucine += 1

    elif (i == "GTT")or(i == "GTC")or(i == "GTA")or(i == "GTG"):
        Valine =+ 1

    elif (i == "TGT")or(i == "TGC"):
        Phenylalanine += 1

    elif (i == "ATG"):
        Methionine += 1

                                                    
if Isoleucine == 1:
    print("ATT ; ATC ; ATA - represents: Isoleucine")

elif Leucine == 1:
        print("CTT ; CTC ; CTA ; CTG ; TTA ; TTG - represents: Leucine")
        
elif Valine == 1:
        print("GTT ; GTC ; GTA ; GTG - represents: Valine")

elif Phenylalanine == 1:
        print("TGT ; TGC - represents: Phenylalanine")

elif Methionine == 1:
        print("ATG - represents: Methionine")

else: print("Codon represents: Amino Acid X")         
In this task I only need to cover the 5 amino acids above, any other codon I can say its represents amino acid X
Reply


Messages In This Thread
List/String seperation issue - by YoungGrassHopper - Sep-19-2019, 01:56 PM
RE: List/String seperation issue - by ichabod801 - Sep-19-2019, 01:58 PM
RE: List/String seperation issue - by perfringo - Sep-20-2019, 06:33 AM
RE: List/String seperation issue - by YoungGrassHopper - Sep-20-2019, 07:57 AM
RE: List/String seperation issue - by perfringo - Sep-20-2019, 08:05 AM
RE: List/String seperation issue - by perfringo - Sep-20-2019, 08:47 AM
RE: List/String seperation issue - by perfringo - Sep-20-2019, 11:17 AM
RE: List/String seperation issue - by perfringo - Sep-20-2019, 11:57 AM

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