print"Enter file name having sequences:";
$filename=<stdin>;
chomp $filename;
print"Enter file name having primer list:";
$primerfile=<stdin>;
chomp $primerfile;
open(PRI,$primerfile) or die"can't open $primerfile";
@primerList=<PRI>;
open(FNM,"$filename") or die"can't open $filename";
@f1=<FNM>;
$f=join('',@f1);
@fnew=split(/>/,$f);
$len=scalar@fnew;

for($k=0;$k<scalar(@primerList);$k++)
{
	@primerList[$k]=uc(@primerList[$k]);
	@primerList[$k]=~s/\n//g;
	@primer=split("",@primerList[$k]);
	$lm=scalar(@primer);
	print "$k seqHavingPrimer_".@primerList[$k].".txt\n";
	open(PAGE,">seqHavingPrimer_".@primerList[$k].".txt") || die"Can't open seqHavingPrimer_@primerList[$k].txt\n";
	for($i=1;$i<$len;$i++)
	{
		$sequence="";
		@fnew_seq=split("\n",@fnew[$i]);
		for($j=1;$j<scalar(@fnew_seq);$j++)
		{
			$sequence.=@fnew_seq[$j];
			$sequence=~s/\s//g;
		}
		$match=0;
		$sequence=uc($sequence);
		if(@primerList[$k]=~/[RYMWSKVHDBN]/)
		{
			for($seq_i=0;$seq_i<length($sequence);$seq_i++)
			{
				#print"\n$i,sequence=$sequence\n";
				$b=substr($sequence,$seq_i,$lm);
				@b=split("",$b);
				for($l=0;$l<scalar(@primer);$l++)
				{
					if(@primer[$l] eq "R"){$pattern="AG";}
					elsif(@primer[$l] eq "Y"){$pattern="TC";}
					elsif(@primer[$l] eq "M"){$pattern="AC";}
					elsif(@primer[$l] eq "W"){$pattern="AT";}
					elsif(@primer[$l] eq "S"){$pattern="CG";}
					elsif(@primer[$l] eq "K"){$pattern="GT";}
					elsif(@primer[$l] eq "V"){$pattern="ACG";}
					elsif(@primer[$l] eq "H"){$pattern="ACT";}
					elsif(@primer[$l] eq "D"){$pattern="AGT";}
					elsif(@primer[$l] eq "B"){$pattern="CGT";}
					elsif(@primer[$l] eq "N"){$pattern="ATGC";}
					else
					{
						@notbraces[$j]++;
						$pattern=@primer[$l];
					}
					if(@b[$l]=~/[$pattern]/)
					{
						$match++;
					}
				}
				if($match==$lm)
				{
					print PAGE ">@fnew[$i]";
					@fnew[$i]="";
					print"match found... in seqHavingPrimer_@primerList[$k].txt\n";
					$seq_i=length($sequence);
				}
				$match=0;
			}
		}
		else
		{
			if($sequence=~/@primerList[$k]/)
			{
				print PAGE ">@fnew[$i]";
				@fnew[$i]="";
				print"match found... in seqHavingPrimer_@primerList[$k].txt\n";
			}
		}
	}
	#close PAGE;
}
open(PAGE2,">seqLackingPrimer.txt") || die"Can't open seqLackingPrimer.txt";
for($i=0;$i<scalar(@fnew);$i++)
{
	if(@fnew[$i] ne "")
	{
		print PAGE2 ">@fnew[$i]";
	}
}
print "Total primer=$k";