CODEWITHSUNDEEP
pythonbioinformatics
Lilly001
Lilly001

Reputation: 1

Count codons in an ORF

I have to write a function count_codons to count the number of times each codon occurs in the ORF.

Desired output:

count_codons('ATGTCATCATGA')

should return

{'CTT': 0, 'ATG': 1, 'ACA': 0, 'ACG': 0, 'ATC': 0, 'AAC': 0,
'ATA': 0, 'AGG': 0, 'CCT': 0, 'ACT': 0, 'AGC': 0, 'AAG': 0,
'AGA': 0, 'CAT': 0, 'AAT': 0, 'ATT': 0, 'CTG': 0, 'CTA': 0,
'CTC': 0, 'CAC': 0, 'AAA': 0, 'CCG': 0, 'AGT': 0, 'CCA': 0,
'CAA': 0, 'CCC': 0, 'TAT': 0, 'GGT': 0, 'TGT': 0, 'CGA': 0,
'CAG': 0, 'TCT': 0, 'GAT': 0, 'CGG': 0, 'TTT': 0, 'TGC': 0,
'GGG': 0, 'TAG': 0, 'GGA': 0, 'TGG': 0, 'GGC': 0, 'TAC': 0,
'TTC': 0, 'TCG': 0, 'TTA': 0, 'TTG': 0, 'TCC': 0, 'ACC': 0,
'TAA': 0, 'GCA': 0, 'GTA': 0, 'GCC': 0, 'GTC': 0, 'GCG': 0,
'GTG': 0, 'GAG': 0, 'GTT': 0, 'GCT': 0, 'TGA': 1, 'GAC': 0,
'CGT': 0, 'GAA': 0, 'TCA': 2, 'CGC': 0}

Here is my code which does not work, what should I change;

Seq1 = 'ATGTCATCATGA'

def count_codons(Seq1):
    split = split_codons(Seq1)#This is my split_codons function, that I will use to split the OFR into a list of codons
    dict_codons = {}
    for codon in split:
        if dict_codons.has_key(codon):
            dict_codons[codon] += 1
        else:
            dict_codons[codon] = 0

Upvotes: 0

Views: 116

Answers (1)

Tranbi
Tranbi

Reputation: 12701

I don't know how you split your sequence but you could use slicing.
Also, collections.Counter will create the kind of dictionary you need:

from collections import Counter

Seq1 = 'ATGTCATCATGA'

def count_codons(seq):
    codons = [seq[i:i+3] for i in range(0, len(seq)-2, 3)]
    return dict(Counter(codons))

print(count_codons(Seq1))

Output:

{'ATG': 1, 'TCA': 2, 'TGA': 1}

If you want to keep entries for codons that are not found in your sequence, create a counter once, then update it:

from collections import Counter
your_counter = {'CTT': 0, 'ATG': 0, 'ACA': 0, 'ACG': 0, 'ATC': 0, 'AAC': 0,
'ATA': 0, 'AGG': 0, 'CCT': 0, 'ACT': 0, 'AGC': 0, 'AAG': 0,
'AGA': 0, 'CAT': 0, 'AAT': 0, 'ATT': 0, 'CTG': 0, 'CTA': 0,
'CTC': 0, 'CAC': 0, 'AAA': 0, 'CCG': 0, 'AGT': 0, 'CCA': 0,
'CAA': 0, 'CCC': 0, 'TAT': 0, 'GGT': 0, 'TGT': 0, 'CGA': 0,
'CAG': 0, 'TCT': 0, 'GAT': 0, 'CGG': 0, 'TTT': 0, 'TGC': 0,
'GGG': 0, 'TAG': 0, 'GGA': 0, 'TGG': 0, 'GGC': 0, 'TAC': 0,
'TTC': 0, 'TCG': 0, 'TTA': 0, 'TTG': 0, 'TCC': 0, 'ACC': 0,
'TAA': 0, 'GCA': 0, 'GTA': 0, 'GCC': 0, 'GTC': 0, 'GCG': 0,
'GTG': 0, 'GAG': 0, 'GTT': 0, 'GCT': 0, 'TGA': 0, 'GAC': 0,
'CGT': 0, 'GAA': 0, 'TCA': 0, 'CGC': 0}

Seq1 = 'ATGTCATCATGA'

def count_codons(seq):
    codons = [seq[i:i+3] for i in range(0, len(seq)-2, 3)]
    return dict(Counter(codons))

your_counter.update(count_codons(Seq1))
print(your_counter)

Output:

{'CTT': 0, 'ATG': 1, 'ACA': 0, 'ACG': 0, 'ATC': 0, 'AAC': 0, 'ATA': 0, 'AGG': 0, 'CCT': 0, 'ACT': 0, 'AGC': 0, 'AAG': 0, 'AGA': 0, 'CAT': 0, 'AAT': 0, 'ATT': 0, 'CTG': 0, 'CTA': 0, 'CTC': 0, 'CAC': 0, 'AAA': 0, 'CCG': 0, 'AGT': 0, 'CCA': 0, 'CAA': 0, 'CCC': 0, 'TAT': 0, 'GGT': 0, 'TGT': 0, 'CGA': 0, 'CAG': 0, 'TCT': 0, 'GAT': 0, 'CGG': 0, 'TTT': 0, 'TGC': 0, 'GGG': 0, 'TAG': 0, 'GGA': 0, 'TGG': 0, 'GGC': 0, 'TAC': 0, 'TTC': 0, 'TCG': 0, 'TTA': 0, 'TTG': 0, 'TCC': 0, 'ACC': 0, 'TAA': 0, 'GCA': 0, 'GTA': 0, 'GCC': 0, 'GTC': 0, 'GCG': 0, 'GTG': 0, 'GAG': 0, 'GTT': 0, 'GCT': 0, 'TGA': 
1, 'GAC': 0, 'CGT': 0, 'GAA': 0, 'TCA': 2, 'CGC': 0}

Upvotes: 1

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