Transcribing DNA exons and append transcripts into a list

Question

I am trying to find a way to read and transcribe a list of DNA sequences (list of lists) only when the for loop finds a start codon (triplet of the list items) and until it finds a stop codon, over and over, but the if function will only transcribe the first codon and won't go through the whole sequence. I'm trying to do this with a mix of normal python and biopython functions cause I think it's simpler.

This is an example:

Start codon: ATG

Stop codon: TAG

gene_1= 'ACGGACTATTC'

gene_2= 'GGCCATGAGTAACGCATAGGGCCC

gene_3=GGGCCCATGACGTACTAGGGGCCCATGCATTCATAG

So, the first gene does not contain any transcript, whereas the second contains 1 and the third contains 2. I'm trying to get rid of everything outside these reading frames and append these transcripts into a list that should look something like this.

mRNAs = ['AGUAACGCA', 'ACGUAC', 'CAUUCA']

This is what I have so far:

genelist=[]

gene_1= 'A','C','G','G','A','C','T','A','T','T','C'
gene_2= 'G','G','C','C','A','T','G','A','G','T','A','A','C','G','C','A','T','A','G','G','G','C','C','C'
gene_3='G','G','G','C','C','C','A','T','G','A','C','G','T','A','C','T','A','G','G','G','G','C','C','C','A','T','G','C','A','T','T','C','A','T','A','G'

genelist.append(gene_1)
genelist.append(gene_2)
genelist.append(gene_3)

def transcription(ORF):
    mRNA= ''
    for i in range(0, len(ORF), 3):
        codon= ORF[i:i+3]
        if codon != 'ATG':
            next(codon)
            if codon == 'ATG':
                mRNA=codon.transcribe()
                if codon == 'TAG':
                    break
    return(mRNA)

mRNAs=[]
for gene in genelist:
    for codon in gene:
        mRNA= transcription(codon)
        mRNAs.append(mRNA)
print(mRNAs)

But it is not really giving anything back, I wonder if the code it's too redundant and I really don't need to define a function here, do you know any better way to do this? Thaaanks!!

Answer 1

I'm afraid none of your code makes much sense. You have written a function that expects an array, and then you are passing it a single letter

for gene in genelist:
    for codon in gene:
        mRNA= transcription(codon)

Then, the function also doesn't make sense. What does next(codon) mean? How would your script know what a codon is or how to move to the next one? And your if codon == 'ATG': is within the if codon != 'ATG': block, so it will never be executed by definition.

I think what you are looking for is something like this, using the same basic approach as your script:

#!/bin/python3
from Bio.Seq import Seq
from Bio.Seq import transcribe 

genelist=[]

gene_1= 'A','C','G','G','A','C','T','A','T','T','C'
gene_2= 'G','G','C','C','A','T','G','A','G','T','A','A','C','G','C','A','T','A','G','G','G','C','C','C'
gene_3='G','G','G','C','C','C','A','T','G','A','C','G','T','A','C','T','A','G','G','G','G','C','C','C','A','T','G','C','A','T','T','C','A','T','A','G'

genelist.append(gene_1)
genelist.append(gene_2)
genelist.append(gene_3)

def transcription(ORF):
    mRNA= ''
    foundStart = False
    foundEnd = False
    for i in range(0, len(ORF), 3):
        codon= "".join(ORF[i:i+3])
        if codon == 'ATG' and not foundStart:
            foundStart = True
        if foundStart and not foundEnd:
            cc=transcribe(codon)
            mRNA = mRNA + transcribe(codon)
        if codon == 'TAG':
            foundEnd = True
       
    return(mRNA)

mRNAs=[]
for gene in genelist:
    mRNA = transcription(gene)
    mRNAs.append(mRNA)
print(mRNAs)

Which returns:

$ foo.py 
['', '', 'AUGACGUACUAG']

Of course, it only returns one mRNA since you only have one gene with an ORF in the 1st frame and your script was only looking at the forward strand and the first frame. In reality, ORFs can be in any of the 6 possible frames. You are also assuming that all ORFs will end with a TAG which is perhaps the case in the species you are working in? I don't remember if there is any genetic code that has TAG as the only stop.

If you do actually need to find ORFs in any frame, then I hope the script above should be enough to get you started.

Answer 2

Just in case this isn't a homework problem, there are already plenty of programs available to do this. One program I use is getorf from the EMBOSS toolkit:

https://emboss.bioinformatics.nl/cgi-bin/emboss/getorf