use strict;
use Bio::SeqIO;

####################################################
#MODULE 1: read protein file, and save it in a hash#
####################################################
my %hash1;
my $sequence = "acids.txt";
my $multifasta = Bio::SeqIO ->new (-file => "<$sequence",-format=> "fasta");
while (my $seq= $multifasta->next_seq()) {
	my $na= $seq->display_id; 	#Saves the ID in $na
	my $des=$seq->description;
	my $ss = $seq->seq; 
$hash1{$na} = $ss;  
}
#############################################################
#MODULE 2: read nucleotide file, and save it in another hash#
#############################################################
my %hash2;
my $genes = "nucleotides.txt";
my $multifasta = Bio::SeqIO ->new (-file => "<$genes",-format=> "fasta");
while (my $seq= $multifasta->next_seq()) {
	my $na= $seq->display_id; 	#Saves the ID in $na
	my $des=$seq->description;
	my $ss = $seq->seq; 
$hash2{$na} = $ss;  
}
#####################
#MODULE 3: my $name;#
#####################
my $name;	 			# Read from standard input
chomp $name;
##########################################################################
#MODULE 4: DOMAIN ANNOTATION + RELATED AMINO ACIDS AND NUCLEOTIDES IN COLUMNS#
##########################################################################
foreach my $name (keys %hash1) {

	my $ac = (split(/\s*\|/, $name))[1];
	#print "$ac\n" ; 

#################################################
#MODULE 4.1: DOMAIN ANNOTATION: POSITION OF DOMAINS#
#################################################
open(FILE, "<" ,"domain.txt");
my @array = (<FILE>);

my @lines = grep (/$ac/, @array);
print for @lines;
close (FILE);
#######################################################
#MODULE 4.2: RELATED AMINO ACIDS AND NUCLEOTIDES IN COLUMNS#
########################################################

	my @array1 = split(//, $hash1{$name}, $hash2{$name});  #CUT SEQUENCE
	my @array2 = unpack("a3" x (length($hash1{$name})),$hash2{$name}); #CUT NUCLEOTIDE SEQUENCE
		my $number = "$#array1+1";


			foreach (my $count = 0; $count <= $number; $count++) {
				print "$count\t@array1[$count]\t@array2[$count]\n";
				


			}	

		}