#usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

# 'shift' removes items from @ARGV
my $nomefile = shift;

print "Insert query:\n";
chomp(my $query = uc <STDIN>);

my $test = Bio::SeqIO->new( -file   => $nomefile,
                            -format => 'fasta');

print "\nResults for $nomefile\n\n";

while (my $seq = $test->next_seq()) {
	my @pos;
	
	my $id = $seq->id;
	my $fasta = uc $seq->seq;
	
	while ($fasta =~ /(?=$query)/g) {
		push @pos, $-[0] + 1;	
	}
	
	if (@pos) {
		printf "%s compare %d volte in posizione @pos with ID %s\n",
			$query, scalar @pos, $id;
	}
	else {
		print "$query does not appear in the sequence with ID $id\n";	
	}
}

##</code><code>##

>chr1
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
TTTATCTTTAGGCGGTATGCACTTTTAACAAAAAANNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCNNNN
>chrM
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAANAATTTCCACC

##</code><code>##

Insert query:
tatt
TATT does not appear in the sequence with ID chr1
TATT    compare 5 volte  in posizione 20 55 152 155 177 with ID chrM