use the join() function to recompose the splitted fields ?

while( my $line = <INPUT> ) {
  # get your columns
  my @fields = split( /\t/, $line );

  doWhatYouWantWith( $fields[0], $fields[1] );

  # recompose your line from the modified columns
  # with a tab separator
  print join( "\t", @fields );
}
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