#!/usr/bin/perl 

use warnings;
use Bio::Perl;
use Bio::Seq;
use Bio::SeqIO;

# Reading the first file and store it into a hash
#the sequence header is stored in the hash key and sequence is stored in the value

my $FastaFile1 = Bio::SeqIO->new(-file => "test.fa", -format => 'fasta', -alphabet => 'dna') or die "Failed to create SeqIO object from \n";

my %fastaH1 =();
while( my $seqFile1 = $FastaFile1->next_seq() ) {
    unless (exists $fastaH1{$seqFile1->display_id."\t".$seqFile1->desc}) {
        $fastaH1{$seqFile1->display_id."\t".$seqFile1->desc} = $seqFile1->seq; #key of the hash is fasta header (all line) and value is sequence.
    }
}

# printing the fasta headers
print "stored fasta headers:\n";
foreach my $key (keys %fastaH1){
		
        print  "$key\n";
	
    }

# reading the codes.txt file and creating the array
open my $file, '<', "codes.txt";
chomp(my @lines = <$file>);
close $file;

print "stored organism codes\n";
foreach (@lines) {
     print " $_\n";
 }

# if each code is found on the hash print match is found
 foreach my $line (@lines) {
	
	chomp $line;
   if(  exists $fastaH1{$line} ){
        print "match found\n";
    }
}