Just copy and paste three or four lines from each file, inside <code> sections, and also a sample of what your desired output is. See Short, Self-Contained Compilable Example or How Do I Post a Question Effectively for hints.

I hope this helps

#Database of table names and new names

Aspergillus_clavatus_1    XP_001276684.1 pectate lyase, putative [Aspe
+rgillus clavatus NRRL 1]
Aspergillus_fumigatus_2    XP_001276694.1 conserved hypothetical prote
+in [Aspergillus fumigatus NRRL 1]
Aspergillus_flavus_3    XP_001276726.1 tyrosinase central domain prote
+in [Aspergillus flavus NRRL 1]
Aspergillus_terreus_4    XP_001276738.1 endoglucanase, putative [Asper
+gillus terreus NRRL 1]

#Lines of the table to be renamed

Aspergillus_clavatus_1    Aspergillus_flavus_198    Aspergillus_terreu
+s_166    Aspergillus_fumigatus_2    
Aspergillus_clavatus_1    Aspergillus_flavus_3    Aspergillus_terreus_
+4    Aspergillus_fumigatus_2
Aspergillus_clavatus_3    Aspergillus_flavus_198    Aspergillus_terreu
+_166    Aspergillus_fumigatus_16


#Expected result (See that in some cases there's no replacement to be 
+done, if the ID is not present in the names "database" file

XP_001276684.1 pectate lyase, putative [Aspergillus clavatus NRRL 1]  
+  Aspergillus_flavus_198    Aspergillus_terreus_166    XP_001276694.1
+ conserved hypothetical protein [Aspergillus fumigatus NRRL 1]    
XP_001276684.1 pectate lyase, putative [Aspergillus clavatus NRRL 1]  
+  XP_001276726.1 tyrosinase central domain protein [Aspergillus flavu
+s NRRL 1]    XP_001276738.1 endoglucanase, putative [Aspergillus terr
+eus NRRL 1]    XP_001276694.1 conserved hypothetical protein [Aspergi
+llus fumigatus NRRL 1]
Aspergillus_clavatus_3    Aspergillus_flavus_198    Aspergillus_terreu
+_166    Aspergillus_fumigatus_16
[download]

Well, I'm still not sure that I really grasp what it is you're trying to do, but maybe this will be of some help. Changes the lines in the second file if the first field in the line is contained as the first field in a line in the first file (combining data from the two files), or does nothing if not:

#!/usr/bin/perl
use strict; use warnings; use feature 'say';
use Data::Dumper;

my @data1 = (
    ['Aspergillus_clavatus_1',  'XP_001276684.1', 'pectate lyase, puta
+tive [Aspergillus clavatus NRRL 1]'],
    ['Aspergillus_fumigatus_2', 'XP_001276694.1', 'conserved hypotheti
+cal protein [Aspergillus fumigatus NRRL 1]'],
    ['Aspergillus_flavus_3',    'XP_001276726.1', 'tyrosinase central 
+domain protein [Aspergillus flavus NRRL 1]'],
    ['Aspergillus_terreus_4',   'XP_001276738.1', 'endoglucanase, puta
+tive [Aspergillus terreus NRRL 1]']
);

my %data1;

for my $record ( @data1 ) {
    my ( $old, $new, $text ) = @{ $record };
    $data1{ $old } = { new => $new, text => $text };
}

my @data2 = (
    ['Aspergillus_clavatus_1', 'Aspergillus_flavus_198', 'Aspergillus_
+terreus_166', 'Aspergillus_fumigatus_2'],
    ['Aspergillus_clavatus_1', 'Aspergillus_flavus_3',   'Aspergillus_
+terreus_4',   'Aspergillus_fumigatus_2'],
    ['Aspergillus_clavatus_3', 'Aspergillus_flavus_198', 'Aspergillus_
+terreu_166',  'Aspergillus_fumigatus_16']
);

my @results;

for my $row ( @data2 ) {
    my $lookup = shift @{ $row };
    push @results, exists $data1{ $lookup } ?
        join "\t", $data1{ $lookup }->{'new'}, $data1{ $lookup }->{'te
+xt'}, join "\t", @{ $row } :
        join "\t", $lookup, join "\t", @{ $row };
}

say Dumper \@results;

__END__
[download]

Output:

$VAR1 = [
          'XP_001276684.1    pectate lyase, putative [Aspergillus clav
+atus NRRL 1]    Aspergillus_flavus_198    Aspergillus_terreus_166    
+Aspergillus_fumigatus_2',
          'XP_001276684.1    pectate lyase, putative [Aspergillus clav
+atus NRRL 1]    Aspergillus_flavus_3    Aspergillus_terreus_4    Aspe
+rgillus_fumigatus_2',
          'Aspergillus_clavatus_3    Aspergillus_flavus_198    Aspergi
+llus_terreu_166    Aspergillus_fumigatus_16'
        ];
[download]

Hope this helps!



The way forward always starts with a minimal test.