monkfan has asked for the wisdom of the Perl Monks concerning the following question:

Most revered monks,
The built-in index function seems to be able to recognize only the first substring given two identical substrings from a string. My code below: 
#!/usr/bin/perl -w
use strict;

my $str = 'NNNNNATCGNNNNATCG';
my @substr  = qw(ATCG ATCG);
foreach (@substr)
{
   my $id = index($str,$_);
   print "$id\n"; 
}

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Returns: 
5
5

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How can I overcome this problem such that the index function can recognize the second substrings in the correct position? Returning this instead: 
5
13

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Regards,
Edward

Replies are listed 'Best First'.
Re: Problem in "index" function in recognizing repeating substrings
by reasonablekeith (Deacon) on Sep 02, 2005 at 09:47 UTC 
    #!/usr/bin/perl -w
use strict;

my $str = 'NNNNNATCGNNNNATCG';
my @substr  = qw(ATCG ATCG);
my $id = -1;
foreach (@substr)
{
   $id = index($str, $_, $id+1);
   print "$id\n"; 
}

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    ---
    my name's not Keith, and I'm not reasonable.
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Re: Problem in "index" function in recognizing repeating substrings
by Tanalis (Curate) on Sep 02, 2005 at 09:35 UTC
    index accepts a position to start from as a third argument. If you track $id to figure out where in the string you are, you should be able to avoid matching the first instance repeatedly.

    See the docs for more information.

    -- Tanalis
    #include www.liquidfusion.org.uk

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Re: Problem in "index" function in recognizing repeating substrings
by ysth (Canon) on Sep 02, 2005 at 12:00 UTC
    Do you want: 
    my $str = "ATCGATCGAT";
my @substr = qw(ATCG CGAT);

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    to give 0 and 2 or 0 and 6?

    If the latter, do 

    $id = -1;
foreach (@substr)
{
   my $id = index($str,$_,$id);
   print "$id\n";
   $id += length($_);
}

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[reply]
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      I've pointed this out to him before, didn't get a response then either.
      ---
      my name's not Keith, and I'm not reasonable.
[reply]
      Dear ysth,
      Thanks a lot for pointing out the important case that I missed.
      With your example above, I will opt for the 'closest' substrings namely: 
      0 and 2

      [download]
      If the latter
      You mean the 'former'? Because, having tested your above code, I think it already gave that answer..
      Please correct me if I'm wrong.

      Regards,
      Edward
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[d/l]
        No, his code clearly gives 0 and 6. If you want 0 and 2, try this: 
        #!/usr/bin/perl
use strict;

my $str = 'ATCGATCGAT';
my @sub = qw(ATCG CGAT);

my $id = 0;

foreach (@sub) {
    $id = index($str, $_, $id);
    print "$id\n";
    $id++;
}

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[reply]
[d/l]

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