#!usr/bin/perl -w

print"\n********Running Fasta34**********  \n \n";
print"\n Please enter the file sequence and library present in your path \n\n";
$result = system("c:/perl/sam/fasta34.exe");
print"\n\n*****enter the output file name you have given***\n";
$output = <STDIN>;
open(FASTA,"c:/perl/sam/$output") or die "cant open the output file \n";


#Make this a function 

#Function1 

#open(FASTA,"c:/perl/sam/$output");
#@ tempseq = <FASTA>;
#$flag=0;
my $var;
my $name;
my $match;
my $seqname;
my @input;
my $iteration;
my $x = 0;
print "Enter your cut off percentage";
$cut = <STDIN>;
while (<FASTA>)
{
	#compare the line of matching sequence 
	if($name = m/>>(.{4,6})(.*)/g)
	{
		$seqname = $1;
		$laterhalf = $2;
	}
	#print "SKIP A LINE iF A MATCH \n";
	next if /^ini/;
	if ($per = m/(\d+\.\d+)% identity/g) 
	{
		$per = $1;
		#check if match is above the cutoff percentage  
		if ($per > $cut)
		{
			print "\n\n$seqname$laterhalf \n";\
			print "identity match $per % \n";
			#store the first line of the input file 
			$input[$x] = "$seqname$laterhalf";
			while(<FASTA>)
			{
				if ($match = m/^($seqname)(.*)/)
				{
					#store the match sequence
					print "$2 \n";
					$input[$x] = $2;		
				}
				if(m/>>/g)
				{
					print @input[$x];
					#open(OUT2IN,">c:/perl/sam/output1");
					#print OUT2IN @input;
					#$iteration = system("OUT2IN");
					$x = $x + 1;
					seek(FASTA,-100,1);
					last;
				}
			}
		}
	}
}
close (FASTA);
print $result;