Hello fellow monks!
I keep trying to understand why I am getting an exception error although it does not seem to be some kind of mistake. So, I have a script that is reading a file and storing some number ranges, which I will use to re-structure a string.
Initial string is something like:
PEGYNDRQAVNGSFYKLTFAPTFKVGSIGDFFSRPEIRFYTSWMDWSKKLNNYA
......................................................

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and, with my script, I will replace the '.' with other characters. The script seems to stumble upon an error in this chunk: 
while ($rest=~/\<REGION seq\_beg\=\"(\d+)\"\s+pdb\_beg\=\"\d+\"\s+seq\
+_end\=\"(\d+)\"\s+pdb\_end\=\"\d+\"\s+type\=\"(\w+)\"\/\>/mg)
{
    $start=$1;
    $end=$2;
    $type=$3;

    $TM_part_to_store = "$start-$end";
    
    $length_part="$start-$end";

    if($type==1)
    { 
        substr($topo_initial, ($start-1), ($end-$start+1), ($side1 x (
+$end-$start+1)));
    }

    elsif($type==2)
    { 
        substr($topo_initial, ($start-1), ($end-$start+1), ($opposite{
+$side1} x ($end-$start+1)));
    }

    elsif($type eq 'B')
    { 
        push @all_TMs_line, $TM_part_to_store; 
    }

    else
    { 
        substr($topo_initial, ($start-1), ($end-$start+1), ('U' x ($en
+d-$start+1)));
    }
}

[download]

where I am getting the info I need and change the '.' accordingly. For debugging, I made the script print the string length and each $start and $end, to see which substring is out of bounds, in the form of string length <TAB> range
Weirdly enough, in the string that it fails, which has a length of 413 characters, the debugging prints the following:
413     1-6
413     7-15
413     16-34
413     35-46
413     47-53
413     54-67
413     68-83
413     84-85
413     86-95
413     96-112
413     113-118
413     119-133
413     134-142
413     143-153
413     154-160
413     161-174
413     175-181
413     182-186
413     187-193
413     194-217
413     218-224
413     225-237
413     238-244
413     245-266
413     267-273
413     274-282
413     283-290
413     291-304
413     305-311
413     312-320
413     321-328
413     329-347
413     348-355
413     356-369
substr outside of string at myscript.pl

[download]

As you can see, for some weird reason, and although my string's length is 413 chars and there are more ranges after 356-369, it exits with this error.
Any ideas?

In reply to substr out of str error - but why? by Anonymous Monk

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