As my duplicate lines tend to be clustered I have tried this code:

while(<INFILE>){
   
    #print "here\n";
    
    if ($_ =~ /^(.{1,50})\t{0,50}(.{0,50})\t{0,1}(.{0,50})\t{0,1}(.{0,
+50})\t{0,1}(.{0,50})\t{0,1}(.{0,50})\t{0,1}(.{0,50})\t{0,1}(.{0,50})\
+t{0,1}(.{0,50})/){
    
    #print "here_B\n";
    
    $bumb = "";

    $gene_id = $1;
    if ($2 =~ /.{1,50}/){ push (@alternative_ids, $2)}
    else{
       push (@alternative_ids, $bumb); 
    }
    
    if ($3 =~ /.{1,50}/){ push (@alternative_ids, $3)}
    else{
        push (@alternative_ids, $bumb);
    }
    
    if ($4 =~ /.{1,50}/){ push (@alternative_ids, $4)}
    else{
        push (@alternative_ids, $bumb);
    }
    
    if ($5 =~ /.{1,50}/){ push (@alternative_ids, $5)}
    else{
        push (@alternative_ids, $bumb);
    }
    
    if ($6 =~ /.{1,50}/){ push (@alternative_ids, $6)}
    else{
        push (@alternative_ids, $bumb);
    }

    if ($7 =~ /.{1,50}/){ push (@alternative_ids, $7)}
    else{
        push (@alternative_ids, $bumb);
    }
    
    if ($8 =~ /.{1,50}/){ push (@alternative_ids, $8)}
           else{
        push (@alternative_ids, $bumb);
    }
    
    if ($9 =~ /.{1,50}/){ push (@alternative_ids, $9)}
    else{
        push (@alternative_ids, $bumb);
    }




    print @alternative_id; 

    foreach (@alternative_ids){
        
        $old_line = $new_line;
        $alternative_id = $_;
        
        $new_line = "$gene_id\t$alternative_id\n"; 
        
        @record_previous_lines = qw/blank/;

        if ($new_line ne $old_line){ #discount consecutive repeats of 
+identical lines
            $switch = 1;

        foreach(@record_previous_lines){
          
            if ($_ =~ /$new_line.$old_line/){
            $switch = 2;
            }
        }
        
        if ($switch = 1){ # don't print lines that have previously bee
+n repeated
            print OUT_B "$new_line$old_line";
        }
        
        if (@record_previous_lines > 200){ # don't let this array get 
+bigger than 200
            shift @record_previous_lines; # shift deletes the first va
+lue of an array
        }
        push (@record_previous_lines, $new_line.$old_lines);
        }
    }
    undef @alternative_ids;
    }
}
[download]

The last bit doesn't seem to be working as I want. Can anyone thow light on this? Sorry I am not being more specific.

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