#!/usr/bin/perl
use strict;
use warnings;

# 'shift' removes items from @ARGV
my $nomefile = shift;
open my $fh, '<', $nomefile or die "Unable to open $nomefile. $!";

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

my $sequenza;
chomp(my $id = <$fh>); # reads first line ('should' be ID)

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

while (my $line = <$fh>) {
	chomp $line;
	
	if (substr($line, 0, 1) eq '>') {		
		find_matches($id, $sequenza, $query);
		
		$sequenza = '';
		$id = $line;
	}
	else {
		$sequenza .= uc $line;	
	}
	
	find_matches($id, $sequenza, $query) if eof;
}

close $fh or die "Unable to close $nomefile. $!";


sub find_matches {
	my ($id, $sequenza, $query) = @_;
	my @pos;
	
	while ($sequenza =~ /(?=$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>##


C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
ttag

Results for fasta.txt

TTAG compare 1 volte in posizione 108 with ID >chr1
TTAG does not appear in the sequence with ID >chrM

C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
aaaaa

Results for fasta.txt

AAAAA compare 3 volte in posizione 59 130 131 with ID >chr1
AAAAA does not appear in the sequence with ID >chrM

C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
tagcgat

Results for fasta.txt

TAGCGAT does not appear in the sequence with ID >chr1
TAGCGAT does not appear in the sequence with ID >chrM