Here is the code I have for opening the file and parsing the tab
@ molecules and @locus are text files which are loaded into arrays

my @locus_small = ();
my $line;

foreach $line (@locus) {

    my @tokens = split(/\t+/, $line);
    unless(scalar @tokens < 6) {
    push(@locus_small, "$tokens[0]\t$tokens[1]\t");
    }
}
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Then I search and print the @found which is based on locus_small but I want the @locus which matched.

So really what I want to do is only search a few columns for a match but print the whole row if there is a match.

foreach my $molecule (@molecules) {

    
    my @found = grep /\Q$molecule\E/i, @locus_small;
    
if (@found) {
        print OUTDATA  ($molecule, ": \n\t", join "\t", @found);
    }
}
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you're doing a lot of extra work in your code. my example below will read your set of locii into an array, create a set of molecules, and print the full locus record if a molecule is found in the first two tokens. records with less than six fields are skipped.

i skip the interim array (@locus_small in your code,) and use nested fors instead of grep, because i think it makes more sense. the really tricky bit is ( @{[]} = split /\s/ ) < 6, but i think my comments should help everyone understand what i'm doing.

the main loop is effectively six lines of code, which should be all you need. oh, and yes, i split on single space instead of tab in my example -- i'm too lazy to change the settings in my editor to spit out tabs instead of spaces ;-) enjoy!

#!/usr/bin/perl -w
use strict;
$|++;


# create phony filehandle named OUTDATA (use STDOUT for debugging)
*OUTDATA = *STDOUT;

# create phony molecule list
my @phony_molecule_list = qw( abc def abcd abc );

# create hash of molecules, to avoid duplicates
my %molecules;

# populate hash of molecules
@molecules{@phony_molecule_list}++;

# create list of locii, from DATA filehandle
chomp( my @locii = <DATA> );

# for each molecule, sorted by longest word first
for my $molecule (sort { length $b <=> length $a } keys %molecules)
{
    LOCUS: for(@locii)
    {
        # skip if less than xxx tokens 
        #   i need to fake out split to get number of fields. usually
        #   you can force list context by () = ..., but this doesn't 
        #   work with split. so, i force split to return its output 
        #   to an anonymous array (list context,) then evaluate the 
        #   anonymous array in scalar context to get number of element
+s.
        next LOCUS if( ( @{[]} = split /\s/ ) < 6 );
        
        # get first two fields (assumes at least three fields exist)
        my($test4match) = ( /(.+?\s.+?)\s/ );
        
        # match a molecule (whole words only), and print the line
        if( $test4match =~ /\b\Q$molecule\E\b/ )
        {
            print OUTDATA $_,$/;
        }
    }
}

__DATA__
abcd ghi 1 2 3 4
xyx yxy a b c
abc xyx z y x w
efg def 5 6 7 8
abc c o
deg abc 9 0
1 abd abc x x
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~Particle *accelerates*