in reply to Find the boundaries of a substring in a string

TIMTOWTDI. Using your code as a starting point I would use pos to find the end point of the sequence. Here is a runnable example.

use strict;
use warnings;

my $seq =
  'dddddddddBBBBBBBBBBBBDDDDDDDDBBBBBBBBBBBBBBddddddddddddddddddddBBBB
+BBBBBBBBBBDDBBBBBBBBddddddddddddd';

while ($seq =~ /(B+)/g) {
    my $seg        = $1;
    my $seg_length = length ($seg);
    my $seg_end    = pos ($seq);
    my $seg_start  = $seg_end - $seg_length;

    print $seg. "|" . $seg_start . "-" . $seg_end . "\n";
}

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Re^2: Find the boundaries of a substring in a string
by Anonymous Monk on Jun 27, 2023 at 09:24 UTC
    Thank you both! I noticed in both snippets that the end boundaries are off by 1, or am I counting wrong?
[reply]

      Are you counting from 1 or zero? If from 1 then it should probably be this (to give the first match at 10 to 21 inclusive):

      use strict;
use warnings;

my $seq =
  'dddddddddBBBBBBBBBBBBDDDDDDDDBBBBBBBBBBBBBBddddddddddddddddddddBBBB
+BBBBBBBBBBDDBBBBBBBBddddddddddddd';

while ($seq =~ /(B+)/g) {
    my $seg        = $1;
    my $seg_length = length ($seg);
    my $seg_end    = pos ($seq);
    my $seg_start  = $seg_end - $seg_length + 1;

    print $seg. "|" . $seg_start . "-" . $seg_end . "\n";
}

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      To say what you expect the answer to be when posting have a read of How to ask better questions using Test::More and sample data.

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[reply]
[d/l]
        Counting from 0, as usual. If you check the first substring, then it starts (correctly) at 9, but it should end at 20, not 21, am I wrong? It has a length of 12, and it includes position 9.
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