Shell Programming and Scripting

CGTGCFTGCGTFREDG
PEOGDKGJDGKLJGKL
DFGDSFIODUFIODSUF
FSDOFJSODIFJSIODFJ
DSFSDFDFSDOFJFOSF
SDFOSDJFOJFPPIPIOP
.
.
.

>sample_1
SDFDSKLFKDSLSDFSDFDFGDSFIODUFIODSUFSDDSFDSSDFDSFAS

>sample_2
DFDFGDSFIODUFIODSUFSDFDSFSDFOSDJFOJFPPIPIOPTPHHPHLHL
.
.

>sample_1
SDFDSKLFKDSLSDFSDFXXXXXXXXXXXXXXXSDDSFDSSDFDSFAS

>sample_2
DFXXXXXXXXXXXXXXXSDFDSFXXXXXXXXXXXXXXXTPHHPHLHL
.
.

sed 's/DFGDSFIODUFIODSUF/XXXXXXXXXXXXXXX/g' input file > output file

cat reference.txt

CGTGCFTGCGTFREDG
PEOGDKGJDGKLJGKL
DFGDSFIODUFIODSUF
FSDOFJSODIFJSIODFJ
DSFSDFDFSDOFJFOSF
SDFOSDJFOJFPPIPIOP

for i in $(cat reference.txt)
do
  sed -i "s/$i/XXXXXXXXXXXXXXX/g" input      # if your sed don't support -i option, replace by below perl command
# or
  perl -i -pe  "s/$i/XXXXXXXXXXXXXXX/g" input 
done

problem 1:
>sample_10
TRAAERASDDSDSTERTRTRTERTEDFGDSFIODU
FIODSUFASDSDASFSAFEDFFDFDFDFDFDFDA
.
.

open FH,"<listfile";
my @tmp = <FH>;
my @pat = map {s/\n//;$_} @tmp;
close FH;
open FH,"<filetobereplaced";
while(<FH>){
  my $str = $_;
  foreach my $pat (@pat){
     my $tmp = $str=~s/$pat/<>/g;
     last if $tmp > 0;
  }
  print $str;
}
close FH;