Shell Programming and Scripting

>Read_1
XXXXXXXXXXSDFXXXXXDS  (condition 1: After the last "X" per line, if the distance is less than or equal to 3 letter, replace those not "X" letter with "X")
TREXXXXXXXSDFXXXXXDS (condition 2: Before the first "X" per line, if the distance is less than or equal to 3 letter, replace those not "X" letter with "X")
.
.

>Read_1
XXXXXXXXXXSDFXXXXXXX
XXXXXXXXXXSDFXXXXXXX
.
.

perl -pe 's/X[^X]{2}$/XXX/g' input

$ 
$ 
$ cat f25
>Read_1
XXXXXXXXXXSDFXXXXXDS
TREXXXXXXXSDFXXXXXDS
XXXXXXXXXXABCXXXXXXW
AQXXXXXXXXPQRXXXXXXX
XXXXXXXXXXDEFXXXXXXX
$ 
$ 
$ perl -lne 'if (/^([^X]{1,3})(X.*)/){($a,$b)=($1,$2); $a=~s/./X/g; print "$a$b"}
             elsif (/^(.*X)([^X]{1,3})$/){($a,$b)=($1,$2); $b=~s/./X/g; print "$a$b"}
             else {print}                                                            
            ' f25
>Read_1
XXXXXXXXXXSDFXXXXXXX
XXXXXXXXXXSDFXXXXXDS
XXXXXXXXXXABCXXXXXXX
XXXXXXXXXXPQRXXXXXXX
XXXXXXXXXXDEFXXXXXXX
$ 
$ 

sed -e 's/\(^X.*\)XDS$/\1XXX/g' -e 's/^TREX\(.*\)/XXXX\1/g' inputfile

sed -e 's/\(^X.*\)XDS$/\1XXX/g' -e 's/^TREX\(.*\)XDS/XXXX\1XXX/g' inputfile