#!/usr/bin/perl

my %ref_h;
my (@refdata,@ar);
my ($start,$end,$format,$col);

open(RF,"<","reffile") or  die "Fail-$!\n";
while (<RF>) {
chomp;
@refdata=split;
push (@{$refdata[0]},$refdata[1],$refdata[2]);
$ref_h{$refdata[0]}=\@{$refdata[0]}
}
close(RF);

open(DF,"<","input_file.txt") or die "Fail-$!\n";
while (<DF>){
        chomp;
        if (/^\>/) {
        ($col=$_)=~s/\>//g;
        next unless exists $ref_h{$col} ;
        print "$_\n";
        next;
        }
        $index=$#{$col};
        for ($k=0;$k<=$index;$k++) {
        $start=$ref_h{$col}[$k];
        $end=$ref_h{$col}[++$k];
        $format="A".($start-1)." x".($end-$start+1)." A*";
        @ar=unpack($format,$_);
        ($ar[1],$ar[2])=("X" x ($end-$start+1),$ar[1]);
        ($_="@ar")=~s/\s//g;
        undef @ar;
        }
        print $_,"\n";
        $start=0;$end=0;$index=0;
}
close(DF);

substr($_,($start-1),($end-$start+1))="X" x ($end-$start);