write a function that only extract certain keys from a dictionary-CodePudding

I want to write a function where any keys can be extracted to give the values. Here is the dictionary and the code that I wrote and the input:

DNAcodon2aa = {"aaa":"K", "aac":"N", "aag":"K", "aat":"N", 
            "aca":"T", "acc":"T", "acg":"T", "act":"T", 
            "aga":"R", "agc":"S", "agg":"R", "agt":"S", 
            "ata":"I", "atc":"I", "atg":"M", "att":"I", 

            "caa":"Q", "cac":"H", "cag":"Q", "cat":"H", 
            "cca":"P", "ccc":"P", "ccg":"P", "cct":"P", 
            "cga":"R", "cgc":"R", "cgg":"R", "cgt":"R", 
            "cta":"L", "ctc":"L", "ctg":"L", "ctt":"L", 

            "gaa":"E", "gac":"D", "gag":"E", "gat":"D", 
            "gca":"A", "gcc":"A", "gcg":"A", "gct":"A", 
            "gga":"G", "ggc":"G", "ggg":"G", "ggt":"G", 
            "gta":"V", "gtc":"V", "gtg":"V", "gtt":"V", 

            "taa":"*", "tac":"Y", "tag":"*", "tat":"T", 
            "tca":"S", "tcc":"S", "tcg":"S", "tct":"S", 
            "tga":"*", "tgc":"C", "tgg":"W", "tgt":"C", 

def translate(codon_list):
  """This function translates a list of codons into a primary amino acid sequence. """
  codon_list = DNAcodon2aa.keys()
  newcodon = ''.join(codon_list)
  protein = ''
  for i in range(0, len(newcodon),3):
      codon = newcodon[i:i 3]
      protein  = DNAcodon2aa[codon]
  return protein

input

translate(['tct','act','gct','gcc'])

output wanted:

'STAA'

output produced

'KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*TSSSS*CWCLFLF'

it gave me the concatenation of all values in the dict instead of the values of certain keys in the input. I have tried and researched all possible codes that I could do but failed. any help would be appreciated.

CodePudding user response：

@quamrana's comment correctly diagnoses the problem with your code. You overwrite codon_list with the keys from DNAcodon2aa. That line should be deleted. It should work after that.

That said, here's a better implementation of your function:

def translate(codon_list):
    return ''.join(DNAcodon2aa[codon] for codon in codon_list)

CodePudding user response：

You need to remove some code from your original function:

def translate(codon_list):
    """This function translates a list of codons into a primary amino acid sequence. """
    protein = ''
    for codon in codon_list:
        protein  = DNAcodon2aa[codon]
    return protein

Results:

>>> print(translate(['tct', 'act', 'gct', 'gcc']))
STAA

CodePudding user response：

Use str.join

def translate(codon_list):
    return ''.join(DNAcodon2aa.get(i) for i in codon_list)

If your input list has some unexpected values and you need to skip the value, you can use it like this.

codon_list = ['tct','act','gct','gcc', 'unexpected']
def translate(codon_list):
        return ''.join(DNAcodon2aa.get(i, '') for i in codon_list)
print(translate)
# 'STAA'