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$ cat > fred.dat
abcd    123     456     defg
cdefg   23              as
        345     235     
xsd             swe

$ perl -Mstrict -Mwarnings -e '
    use Tie::File;
...
    @fred_data = map { s/(^|\t)(?=\t|$)/${1}Missing/g; $_ } @fred_data
+;
    untie @fred_data;
'

$ cat fred.dat
abcd    123     456     defg
cdefg   23      Missing as
Missing 345     235     Missing
xsd     Missing swe     Missing