Shell Programming and Scripting

#!/usr/bin/perl -w

use Switch;

print "PLEASE ENTER THE FILENAME OF THE FILE:=";
chomp($prot_psap=<STDIN>);

open(PROTFILE,$prot_psap) or die "unable to open the file";
@prot=<PROTFILE>;
close PROTFILE;
foreach $line (@prot) {

#$line ="s/*//g";
if ($line =~ s/^>//g) {
next;
}
else {
$sequence = $line;
}
$sequence  =~ s/\*/ /g;

@prota=split('',$sequence);
print @prota;
}

print "PLEASE ENTER THE FILENAME OF THE FILE:=";
chomp($mutation_file=<STDIN>);

open(MUTFILE,$mutation_file) or die "unable to open the file";
@mut=<MUTFILE>;
close MUTFILE;

foreach $line (@mut) {
if ($line =~ s/^>//g) {
next;
}
else {
$mutation = $line;
#$i=0;
}
$mutation  =~ s/[^A-Z]/ /g;


@muta=  split('',$mutation);

print @muta,"\n";
}

my %hash=(A,1,C,2,D,3,E,4,F,5,G,6,H,7,I,8,K,9,L,10,M,11,N,12,P,13,Q,14,R,15,S,16,T,17,V,18,W,19,Y,20);
open $fh,"<","a.spl";
my %hash1;
while(<$fh>){
	my @tmp=split(/\*/,$_);
	for(my $i=0;$i<=$#tmp;$i++){
		$hash1{$.}->{$i+1}=$tmp[$i];
	}
}
close $fh;
open $fh,"<","a.txt";
while(<$fh>){
	my @tmp=split("",$_);
	map {print $_,"=",$hash1{$.}->{$hash{$_}},"," if $_=~/[A-Z]/} @tmp;
	print "\n";
}