#!usr/bin/perl -w

print"\n********Running Fasta34**********  \n \n";
print"\n Please enter the file sequence  \n";
my $seqfile = <STDIN>;
print "\n Please Enter the library file name \n";
my $library = <STDIN>;

#my $library = defined $ARGV[1] ? $ARGV[1] : "$default_library"; 
# get library from command line, or use default
my $output = "c:/perl/sam/out.fasta";
open(FASTA,"$output") or die "cant open the output file \n";
$result = system("c:/perl/sam/fasta34.exe -Q $seqfile $library -o $output");
#print"\n\n*****enter the output file name you have given***\n";
#$output = <STDIN>;

my $seqname;
my $iteration;
my $orig = "c:/perl/sam/orginal.fasta";
my $out2in = "c:/perl/sam/output1.aa";
my $compare = "c:/perl/sam/compare.fasta";
print "Enter your cut off percentage";
$cut = <STDIN>;
while (<FASTA>)
{
	#compare the line of matching sequence 
	if(m/>>(.{4,6})(.*)/)
	{
		$seqname = $1;
		$laterhalf = $2;
	}
	#print "SKIP A LINE iF A MATCH \n";
	next if /^ini/;
	if (m/(\d+\.\d+)% identity/) 
	{
		$per = $1;
		#check if match is above the cutoff percentage  
		if ($per > $cut)
		{
			#print "\n\n$seqname$laterhalf \n";\
			#print "identity match $per % \n";
			#store the first line of the input file 
			open(ORG,">>$orig");
			open(OUT2IN,">$out2in");
			print OUT2IN "$seqname$laterhalf \n";
			print ORG "$seqname$laterhalf \n";
			while(<FASTA>)
			{
				if (m/^($seqname)(.*)/)
				{
					#store the match sequence
					print OUT2IN "$2 \n";
					print ORG "$2 \n";
				}
				if(m/>>/)
				{
					#print "end of given loop";				
					print "rerunning the fasta program";
					$iteration = system("c:/perl/sam/fasta34.exe -Q $out2in $library -O $compare");
					open(COMPARE,$compare);
					seek(FASTA,-100,1);
					last;
					
				}
			}close(OUT2IN);
		}
	}
}
close (FASTA);
close (COMPARE);
print $result;
#print $iteration;