Question

I am iterating through a file and on each line I am looking for a regex. If the regex is found I just want to print “it’s found” and then the index location of where it was found in that line.

Example:

looking for: 'HDWFLSFKD' need index between two Ds
line: MLTSHQKKF*HDWFLSFKD*SNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
output: 'its found' index location: 10-17

The above ‘looking for’ is quite simple but I am planning to have complex regex statements in there.
So basically Just want to know if a regex is found in a string then how do we get the index location of it?

Here is the code I have so far:

foreach my $line (@file_data)
{
        if ($line=~ /HDWFLSFKD/){
            print "it's found\n"; 
            print "but at what index are the two Ds";
          }   
        else {
            $sequence.=$line;
            print "came in else\n";
        }
}

Answer 1

I believe you are looking for pos:

 #!/usr/bin/perl

use strict;
use warnings;

my $sequence;
while (my $line = <DATA>) {
    if ($line=~ /(HDWFLSFKD)/g){
        print "its found index location: ", 
            pos($line)-length($1), "-",  pos($line), "\n";
    } else {
        $sequence .= $line;
        print "came in else\n";
    }
}

__DATA__
MLTSHQKKF*HDWFLSFKD*SNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSK*HDWFLSFKD*QNHSIKDIFNRFNHYIYNDLGIRTIA

You can also use the @- and @+ variables:

#!/usr/bin/perl

use strict;
use warnings;

my $sequence;
while (my $line = <DATA>) {
        if ($line=~ /HDWFLSFKD/){
                print "its found index location: $-[0]-$+[0]\n";
        } else {
                $sequence .= $line;
                print "came in else\n";
        }
}

__DATA__
MLTSHQKKF*HDWFLSFKD*SNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSK*HDWFLSFKD*QNHSIKDIFNRFNHYIYNDL