Question

I have written the following code in Perl. I want to iterate through a string 3 positions (characters) at a time. If TAA, TAG, or TGA (stop codons) appear, I want to print till the stop codons and remove the rest of the characters.

---

Example:

data.txt

ATGGGTAATCCCTAGAAATTT

ATGCCATTCAAGTAACCCTTT

Answer:

ATGGGTAATCCCTAG (last 6 characters removed)

ATGCCATTCAAGTAA (last 6 characters removed)

(Each sequence begins with ATG).

---

Code:

#!/usr/bin/perl -w

open FH, "data.txt";
@a=<FH>;

foreach $tmp(@a)
{
  for (my $i=0; $i<(length($tmp)-2); $i+=3)
  {
    if ($tmp=~/(ATG)(\w+)(TAA|TAG|TGA)\w+/)
    {
      print "$1$2$3\n";
    }
    else 
    { 
      print "$tmp\n"; 
    }
    $tmp++;
  }
}
exit;

However, my code is not giving the correct result. There should not be any overlaps in the characters (I want to move every 3 characters).

Can someone suggest how to fix the error?

Thanks!

Answer 1

Script:

#!/usr/bin/perl

use strict;
use warnings;

open FH, "data.txt";
my @a = <FH>;

foreach (@a) {
  print /^(ATG(...)*?(TAA|TAG|TGA))/? $1 : $_, "\n";
}

Output:

ATGGGTAATCCCTAG
ATGCCATTCAAGTAA