#!/usr/bin/perl -w
    use strict;
    use Getopt::Long;
     
    #usage example: perl GetbackIDs.pl -p /path_to_files -e [table file extension]
    #requires a table file and a "IDs database" in ".txt" format that share their name
    my ($path, $ext);
    GetOptions(
        'path=s'      => \$path,
        'extension=s' => \$ext,
        );
       
    print "$path\n";
    chdir $path or die "ERROR: Unable to enter $path: $!\n";
    opendir (TEMP , ".");
    my @files = readdir (TEMP);
    closedir TEMP;
    print "@files\n";
     
    my $name;
    my @db;
    for my $file (@files) {
        if($file=~/(\w+).$ext/){
            $name = "$1";
            print"This is the Filename: $file\n";
            open (INFILE, "$file") || die ("cannot open input file");
            chomp(my @data = <INFILE>);
            my$file2= "$name.bd";
            print"This is the DBname:$file2\n";
            open (DB, "$file2") || die ("cannot open input file");
            chomp(@db = <DB>);    
        }    
    #Edition "on the fly" via One-Liner
    for(@db){
            my ($dbid,$firstid) = split(/\t/, $_);
            chomp $firstid;
            print"This is my $dbid and its $firstid\n";
            ##ONELINER #if id matches, replace id
            my$susti=`perl -pi -e 's/$dbid/$firstid/g' $name.$ext`;
            }
        }


##</code><code>##

#Database of table names and new names

Aspergillus_clavatus_1	XP_001276684.1 pectate lyase, putative [Aspergillus clavatus NRRL 1]
Aspergillus_fumigatus_2	XP_001276694.1 conserved hypothetical 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, putative [Aspergillus terreus NRRL 1]

#Lines of the table to be renamed

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


#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 flavus NRRL 1]	XP_001276738.1 endoglucanase, putative [Aspergillus terreus NRRL 1]	XP_001276694.1 conserved hypothetical protein [Aspergillus fumigatus NRRL 1]
Aspergillus_clavatus_3	Aspergillus_flavus_198	Aspergillus_terreu_166	Aspergillus_fumigatus_16