#!/usr/bin/perl 
#ENTERING A MOTIF TO BE SEARCHED FROM USER INPUT
print "Enter a pattern to be searched:";
$seq =<STDIN>;
chomp($seq);
@seqss = split ('',$seq);
$m=scalar @seqss;
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[$m-1];
#ASSIGNING KEY VALUES TO MOTIFS
my @unique = ();
my %seen   = ();
@pats=reverse @seqss;
foreach my $elem ( @pats )
{
next if $seen{ $elem }++;
push @uni, $elem;
@unique= reverse @uni;
}
$cc=1;
foreach (@uni)
{
	$count{$_} = $cc;
	$cc++;
}
$zen = $m+1;
for(my $i=0;$i<scalar @unique;$i++)
{
$mcut=scalar @unique;
$m=$mcut-$i;
%num=("$unique[$i]"=>"$m");
while (($key1, $val1) = each(%num))
{
push(@key,$key1);
push(@val,$val1);
}
}
#OPENING A DATABASE (A TEXT FILE WHERE STRINGS OF ALPHABETS SAVED)
open (PIR,'/home/httpd/heidi/fasta/pir/heidi_pir/pirdb.txt');
$count=0;
while (<PIR>)
{
	if (/^ENTRY/)
		{$entry = $_;}
	elsif (/^>gi/)
		{$gi = $_;}
	elsif(/^TITLE/)
		{$title = (s/                   /\n\t\t /g,$_);}
	elsif(/^ORGANISM/)
		{$org = (s/                   /\n\t\t /g,$_);}
	elsif(/^ACCESSIONS/)
		{$acc = $_;}
	else
	{
		@array2 = $_;
	}
	#what i need is only this from the database (ie., the string where i have to match the motif or pattern)
	if (defined $array2[0])
	{
		@onlyseq = split('',$array2[0]);	
	}
	@array2=();
	#ASSIGNING KEY VALUES FOR THE STRING INCLUDING MOTIFS(VALUES)
	foreach $_(@onlyseq)
	{
		if($count{$_} != $zen)
		{
			if (defined $count{$_})
			{
				push(@a,$count{$_});
				push(@b,$_);
				#print @a;
				#print @b;
			}
			else
			{
				push(@a,$zen);
				push(@b,$_);
				#print @a;
				#print @b;
			}
		}
				
	}
	#SEARCHING FOR MOTIFS IN THE STRING<< THIS IS WHERE I AM STUCK WITH>>
		$m=scalar @seqss;
		for(my $i=$m;$i<=scalar @a;$i++)
		{
		#COMPARING THE LAST AND THE FIRST CHARACTER
			if(($lastch eq $b[$i]) && ($firstch eq $b[$i-($m-1)]))
			{
			#I WANT TO COMPARE THE INBETWEEN CHARACTERS HERE ITSELF.((( WHERE I NEED YOUR HELP)))
				#for(my $j=($i-($m-1));$j<=$i;$j++)
				#{
				#	push(@fnum,$a[$j]);
				#	push(@flet,$b[$j]);
				#}
				#$t=$i+1;
				#$i=$t+$i-1;
				
			}
		}
		$m=scalar @seqss;
		while (@flet) 
		{ 
			push(@words, join('', splice(@flet, 0, $m))); 
		}
		#print "@words\n";
		foreach (@words)
		{
		next unless $_ =~ /$seq/; 
		print("$_\n");
		$count++;
		}	
		@onlyseq=();
		@a=();
		@b=();
		@flet=();
		@fnum=();
		@words=();
}
print "\nThe number of patterns found in PIR database : $count\n";

##</code><code>##

ENTRY            CCHU       #type complete
TITLE            cytochrome c [validated] - human
ORGANISM         #formal_name Homo sapiens #common_name man
ACCESSIONS       A31764; A05676; I55192; A00001
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCCZ       #type complete
TITLE            cytochrome c - chimpanzee (tentative sequence)
ORGANISM         #formal_name Pan troglodytes #common_name chimpanzee
ACCESSIONS       A00002
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCMQR      #type complete
TITLE            cytochrome c - rhesus macaque (tentative sequence)
ORGANISM         #formal_name Macaca mulatta #common_name rhesus macaque
ACCESSIONS       A00003
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
ENTRY            CCMKP      #type complete
TITLE            cytochrome c - spider monkey
ORGANISM         #formal_name Ateles sp. #common_name spider monkey
ACCESSIONS       A00004
GDVFKGKRIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQASGFTYTEANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE