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List/String seperation issue
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List/String seperation issue
#11
(Sep-20-2019, 08:47 AM)perfringo Wrote: It's unclear where III comes from.

But maybe this can help:

(1) Create datastructure to hold sequences:

amino_acids = {**dict.fromkeys(['ATT', 'ATC', 'ATA'], 'Isoleucine'), 
               **dict.fromkeys(['CTT', 'CTC', 'CTA', 'CTG', 'TTA', 'TTG'], 'Leucine'), 
               **dict.fromkeys(['GTT', 'GTC', 'GTA', 'GTG'], 'Valine'),
               **dict.fromkeys(['TTT', 'TTC'], 'Phenylalanine'), 
               **dict.fromkeys(['ATG'], 'Methionine')}
amino_acids is dictionary where DNA codon is key and value is corresponding amino acid:

# amino_acid
{'ATT': 'Isoleucine',
 'ATC': 'Isoleucine',
 'ATA': 'Isoleucine',
 'CTT': 'Leucine',
 'CTC': 'Leucine',
 'CTA': 'Leucine',
 'CTG': 'Leucine',
 'TTA': 'Leucine',
 'TTG': 'Leucine',
 'GTT': 'Valine',
 'GTC': 'Valine',
 'GTA': 'Valine',
 'GTG': 'Valine',
 'TTT': 'Phenylalanine',
 'TTC': 'Phenylalanine',
 'ATG': 'Methionine'}


(2) Chunk DNA sequence:

x = 3
dna = 'ATTCTTTTCATGCTCCTGTTACTAAA'
chunks = [dna[y-x:y]  
         for y in range(x, len(dna)+x, x)  
         if len(dna[y-x:y]) == 3] 
Which nicely chops off trailing AA-s:

['ATT', 'CTT', 'TTC', 'ATG', 'CTC', 'CTG', 'TTA', 'CTA']
(3) Iterate over chunks and replace sequence with amino acid:

>>> [amino_acids[sequence] for sequence in chunks]
['Isoleucine',
 'Leucine',
 'Phenylalanine',
 'Methionine',
 'Leucine',
 'Leucine',
 'Leucine',
 'Leucine']

My goodness perfringo , your skills astound me, you sorted this in 2 ticks , only problem is I will not be able to take credit for this work, I will not be able to sleep at night if I had to tell my mentor this was my creation haha. Amazing solution. I only recently learned about dictionaries, and I have never seen it used like that as in the very top section of the code. I will have to read up on it. the basic dictionary below that makes sense to me though.
Thanks for your superb support you are golden
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 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 YoungGrassHopper - Sep-20-2019, 09:25 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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