I have 2 files, genomic_dna,txt and exons.txt.
The first file contains the genomic DNA sequence of interest and the second file contains the start and stop codons of the exons.
I want to import the two files and splice the exons out of the DNA sequence to then concatenate them together but I am not sure how to splice it.
At first this is what I tried which worked but it did not use the second file:
#read the file containing the genomic dna
file = open("genomic_dna.txt", "r")
#create the file object
contents = file.read()
#extract the exons from the genomic dna
ex1 = contents[5:58]
ex2 = contents[72:133]
ex3 = contents[190:276]
ex4 = contents[340:398]
#concatenate the exons
DNA_Exons = ex1 + ex2 + ex3 + ex4
#open a new file for the exons
file2 = open("DNA_exons.txt", "w")
#write the exons in the new file
file2.write(DNA_Exons)
Then I tried to use the second file as part of my code but I keep getting an error message;
#read the file containing the genomic dna
file2 = open("exons.txt", "r")
#create the file object
contents = file.read()
contents2 = file2.read()
#get the exon positions from exons.txt
for line in file2:
position_list = line.split(",")
start = position_list[0]
end = position_list[1]
with open("genomic_dna.txt", "r") as file:
contents = file.read()
exon = contents.split(start, end)
print(str(exon))
TypeError: 'str' object cannot be interpreted as an integer
However the .split() function can only contain integers not a variable, is there a way I can get around this as that keeps throwing an error? I also tried the normal splicing like this:
exon = contents[start:end]
TypeError: slice indices must be integers or None or have an __index__ method
But again, you can only use integer indexes as the error message showed.