I would use HTML::TokeParser to pull the links out of your file and then modify them from there, like so

#!/usr/bin/perl -w
use HTML::TokeParser;
use strict;

my $i=0;
## set marker definintions
my @markers = qw/ anfnf11 iopi1p83288 9032-jjjf /;
my $htmlfile = "index.html";
my $content;

## get contents of your html file
open (FILE," $htmlfile") || die "Cannot open HTML file for parsing!: $
+!\n";
while(<FILE>) {
        $content .= $_;
}
close(FILE);

my $parse = HTML::TokeParser->new(\$content);
while (my $token = $parse->get_tag("a")) {
        my $url = $token->[1]{href} || "-";     ## put link into $url
        my $text = $parse->get_trimmed_text("/a");      ## put link de
+sc into $text
        if ($markers[$i]) {
                print "<a href=$url/$markers[$i]>$text</a>\n";
        } else {
                ## no more markers...
        }
        $i++;
}
exit;
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-p

open (FILE," $htmlfile") || die "Cannot open HTML file for parsing!: $
+!\n";
while(<FILE>) {
  $content="$content$_\n";
}
close(FILE);
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This construct is not ideal. You are interpolating the variable $content into a new string for every line. You should use concatenation and just append to the string:

while(<FILE>) {
  $content .= "$_\n";
}
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But what you are doing now is slurping in the whole file and adding an extra newline at the end of each line (for which I see absolutely no reason). The same thing can be achieved by undefing $/ like this:

{
  local $/; # undefs $/ for this block of code only

  open (FILE," $htmlfile") || die "Cannot open HTML file for parsing!:
+ $!\n";

  $content = <FILE>; # reads in whole file

  $content =~ s/\n/\n\n/g; # if really necessary to duplicate newlines

  close(FILE);
}
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-- Hofmator

How about just $content = join'', <FILE>; No need to mess with $/ and have to remember to localise it. Wo betide he who forgets to localise $, $" $/ $\

Update

As chipmunk points out this is slower than undef $/ for the gory details see Re: Re: Re: Re: Re: appending a unique marker to each url in a file. For big files the difference is significant, for small ones it is negligible but who wants to paint themselves into a scaling corner? It is better to undef $/, just remember to localise it.

Ugh posted bad code again.

cheers

tachyon

s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print

$pos = 0;
while ($m = shift @markers) {
    # locate the beginning of the link
    last if (($pos = index $htmlfile, '<a', $pos) < 0);
    # ...then the start of the link's href
    last if (($pos = index $htmlfile, 'href="', $pos) < 0);
    # skip past the first "
    $pos += 6;
    # ...then the end of the quoted href target
    last if (($pos = index $htmlfile, '"', $pos) < 0);
    substr($htmlfile, $pos, 0) = $m;
}
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At the end, $pos will be -1 and @markers will be empty if you ran out of links before you ran out of markers. If $pos is not -1, do one more index looking for <a and/or href=. If it hits (i.e., does not return -1), you ran out of markers before all of the links were done. If it does return -1, your links and @markers matched up perfectly.

Update: Woops, my ending logic was broken (it's fixed now). The final index check has to be done if $pos is not -1, not just if there's anything left in @markers as I originally stated.

$htmlfile =~ s/<a\s+href\s*=\s*(["']?)(http.*?)\1>/
               @markers or die "More URLs than markers.\n";
               qq{<a href="$2} . shift(@markers) . '">'/gie;

@markers and die "More markers than URLs.\n";
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this a link: <br> <a href="http://www.somewhere.org/foo">somewhere</a>
+<p> <a href= https://somewhere.else.net/bar/>another place to go</a>.
+<p>
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this a link: 
http://www.somewhere.org/foo
another place to go:
https://somewhere.else.net/bar/
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#$unprocessed_html holds the text of the html version of my file
#$unprocessed_text holds the plain text version of my file
#@markers holds the unique url markers, ie [/qfk33pe][/nnd92093]
  
  #handle html version
  my $processed_html = "";
  
  while (length($unprocessed_html) > 0) {
    
    if($unprocessed_html =~ s/^(.*?\b(href|action)\s*=\s*)//si) {
      $processed_html .= $1;
    } else {
      $processed_html .= $unprocessed_html;
      last;
    }
    
    if (not(@markers)){
      $processed_html .= $unprocessed_html;
      warn "no more markers available for remaining links\n";
      last;
    }
    
    if($unprocessed_html =~ s/^([^\"\'][^<>\s]*)//) {
      my $url = $1 . shift(@markers);
      #strip double //s due to sloppy input
      $url =~ s|//|/|g;
      $processed_html .= $url;
      
    } elsif($unprocessed_html =~ s/^([\"\'])([^<>]*?)\1//) {
      my $url =  $1 . $2 . shift(@markers) . $1;
      #strip double //s that can result from sloppy input
      $url =~ s|//|/|g;
      $processed_html .= $url;
    } else {
      die "something happened here";
    }
    
  }
  
  #handle text version  
  my $processed_text = "";
  while (length($unprocessed_text) > 0) {
    
    if($unprocessed_text =~ s/^(.*?\b)http/http/si) {
      $processed_text .= $1;
    } else {
      $processed_text .= $unprocessed_text;
      last;
    }
    
    if (not(@markers)){
      $processed_text .= $unprocessed_text;
      warn "no more markers available for remaining links\n";
      last;
    }
    
    if($unprocessed_text =~ s/(http[\S]+)\s+//){
      my $urlfound = $1 . shift (@markers);
      $urlfound =~ s|//|/|g;
      $processed_text .= "$urlfound\n";
      
    } elsif($unprocessed_text =~ s/(http[\S]+)$//){
      my $urlfound = $1 . shift (@markers);
      $urlfound =~ s|//|/|g;
      $processed_text .= "$urlfound\n";
    }
    
  }
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