How to count multiple characters from a string using Python

Question

I want to count how many basic cracks of the type ATC (for example) have in sequence seq.

What I’ve done so far is:

# CONTAGEM DE NUCLEOTIDEOS
# CONTAGEM DE TRINCAS/CÓDONS DE UMA SEQUENCIA seq

seq = 'ATC CAA GTC AGC TAG CGT ATC ATC GTC ATG CTC AAA CAC TAC GAT GCT AAT'.replace(" ", "")

conta = contt = contc = contg = contador = contATC = 0

for x in seq:
    if x == 'A':
      conta += 1
    if x == 'T':
      contt += 1
    if x == 'C':
      contc += 1
    if x == 'G':
      contg += 1
    if x == 'ATC':       # trinca ATC
      contATC += 1

    contador += 1  # total

print(f'''A quantidade de nucleotideos "A" é {conta},
      de "T" é {contt}, de "C" é {contc}, de "G" é {contg},"ATC" é {contATC}
      assim, o total foi {contador}.''')

You can criticize me constructively about other things too, I’m open to learning!

Answer 1

If the cracks are separated by space, an alternative is to separate them using split and count how many are equal to "ATC":

seq = 'ATC CAA GTC AGC TAG CGT ATC ATC GTC ATG CTC AAA CAC TAC GAT GCT AAT'
atc = 0 # quantidade de ATC
for s in seq.split():
    if s == 'ATC':
        atc += 1

Already to count the letters individually, you can use a Counter:

from collections import Counter
c = Counter(seq)

And to get the totals just catch them from the Counter:

print(f'A quantidade de nucleotideos "A" é {c["A"]}, de "T" é {c["T"]}, de "C" é {c["C"]}, de "G" é {c["G"]}, de "ATC" é {atc}')

As for the overall total, it would be sufficient to add up the values of the Counter, ignoring the spaces:

total = sum(qtd for s, qtd in c.items() if s in ('A', 'T', 'C', 'G'))

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Detail: when you iterate for a string (as in for x in seq), with each iteration the x will be one of the characters of the string, and therefore it will never be equal to "ATC". Therefore, your code will not work.

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Now if you don’t have spaces, an alternative is to iterate through the string and pick up pieces 3 by 3:

seq = 'ATCGATCTA'
atc = 0
for i in range(0, len(seq), 3):
    if seq[i:i + 3] == 'ATC':
        atc += 1

I use the syntax of slicing to pick up a particular string snippet: seq[i:i + 3] take 3 characters from position i, and the i goes from zero to string size, jumping from 3 to 3. That is, in the example above I get first "ATC", then "GAT" and then "CTA", and therefore the amount of "ATC" will be 1.

In the comments you said you used count, but beware that can make a difference. For the above example, seq.count('ATC') results in 2, because "ATC" occurs 2 times in the string:

ATCGATCTA
^^^ ^^^
 |   |
 |   \_ segunda ocorrência
 \_____ primeira ocorrência

Only that the second occurrence I understand is wrong, because the "AT" is part of the three "GAT" and the "C" is part of the "CTA", so in fact it is not an occurrence of "ATC".