You could do it in two phases: 
use 5.006000;  # Perl 5.6.0+

use strict;
use warnings;

use Regexp::List ();

my $txt;

{ # Remove comments.
   open(my $txtfh, '<', $txtf)
      or die("Can't open $txtf : $!\n");

   # Read entire file into memory.
   local $/;
   $txt = <$txtfh>;

   $txt =~ s{/\*.*?\*/}{}sg;  # Remove comments.
   $txt =~ s{/\*.*/}{}s;      # Remve unmatched comment.
}

my @matches = ...;

my $regexp = Regexp::List
             ->new(modifiers => 'i', quotemeta => 0)
             ->list2re(@matches);

open(my $txtfh, '<', \$txt);

while (my $line = <$txtfh>) {
   my @fld = split(/\|/, $line);
   print "$fld[0] $fld[2] sequence=$fld[4] $fld[5]"
      if $line =~ $regexp;
}

[download]

Update: Oops! holli already posted the same thing.

In reply to Re: while loop logic by ikegami
in thread while loop logic by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.