UPDATE: I decided that this is not right. The read of the very last line will consume all characters and hence reach eof. So you can reach eof before a read of <MAPPINGFILE2> would return an undef (the normal way to detect eof).

              while (<MAPPINGFILE2>) {

                    chomp();
                    # Skip blank lines and comments
                    next if /^(\s*(#.*)?)?$/;

                    # Split mapping columns (tab)
                    @mapping = split /\t/, $_;

                    # Mapping is matching
                    if ($line =~ m/$mapping[0]/) {

                        $line =~ s/$mapping[0]/$mapping[4]/;
                        @source = split /\t/, $line;
                        $line =~ s/$source[2]/$mapping[2]\tALLOC_$sour
+ce[2]/;
                        push @lines2, $line;
                        last;
                    } elsif (eof(MAPPINGFILE2)) { #correction: ###### 
+Can happen 
                        push @rejects, "Lignes non mappées (Account): 
+"."\t".$line;
                    }
                }
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