#!usr/bin/perl -w

print"\n********Running Fasta34**********  \n \n";
print"\n Please enter the file sequence  \n";
my $seqfile = <STDIN>;
#initial file querry sequence
print "\n Please Enter the library file name \n";
#initial library 
my $library = <STDIN>;
my @orgarr;
my @inparr;
my $recall;
my $main = "c:/perl/sam/main.fasta";
#main.fasta stores the output to the fasta program
$result = system("c:/perl/sam/fasta34.exe -O $main -Q $seqfile $library");
if ($result >> 0)
{	
	warn "fasta34.exe ended with non-zero exit status \n";
}
open(FASTA,"$main") or die "cant open the output file \n";
my $seqname;
my $org = "c:/perl/sam/orginal.fasta";
#original.fasta stores the header and the sequences of all the matches in fasta file
my $input = "c:/perl/sam/input.txt";
#input.txt  stores the header and the sequences of matches above cut off
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 $per % \n";
			#store the first line of the input file 
			open(ORG,">>$org");
			open(INPUT,">>$input");
			print INPUT ">$seqname$laterhalf \n";
			print ORG ">$seqname$laterhalf \n";
			
			#print all the sequences which matched the cutoff
			while(<FASTA>)
			{
				if (m/^($seqname)(.*)/)
				{
					#store the match sequence
					print INPUT "$2 \n";
					print ORG "$2 \n";
				}
				if(m/>>/)
				{
					#check if next sequence if so rewind one line back";				
					seek(FASTA,-100,1);
					#break command
					last;
 				}
			}
			print INPUT "\n";
			print ORG "\n";
			close(INPUT);
			close(ORG);
		}
		else
		{
			#printing all the sequences which is showed in fasta o/p file
			open(ORG,">>$org");
			print ORG ">$seqname$laterhalf \n";
			while(<FASTA>)
			{
				if (m/^($seqname)(.*)/)
				{
					#store the match sequence
					print ORG "$2 \n";
				}
				if(m/>>/)
				{
					#print "end of given loop";				
					seek(FASTA,-100,1);
					last;
				}
			}
			print ORG "\n";
			close(ORG);
		}
		
	}
	
	
	
	
}
close (FASTA);
open(ORG,"$org");
open(INPUT,"$input");
@inparr = <INPUT>;
@orgarr = <ORG>;
close(INPUT);
close(ORG);

$length=@inparr;
print "length of inparr array is $length \n";
$querry = "c:/perl/sam/querry.aa";
$compare = "c:/perl/sam/compare.fasta";
$segcompare = "c:/perl/sam/segcompare.txt";
my $seqname1;
my $laterhalf1;
open(QUERRY,">$querry") or die "cannot open querry file\n";
open(SEGCOMPARE,">$segcompare") or die "cannot open segcompare file\n";;
my $temp=0;

while($temp<=$length)
{
	
	while ($inparr[$temp] ne "\n")
	{
		print QUERRY "$inparr[$temp]";
		$temp++;
	}
	
	$recall = system("c:/perl/sam/fasta34.exe -O $compare -Q $querry $library");
	print "hi \n";
	if ($recall > 0)
	{	
		warn "fasta34.exe ended with non-zero exit status \n";
	}
		
	open(COMPARE,"$compare")or die "cant open the output file \n";
	while(<COMPARE>)
	{
		if(m/>>(.{4,6})(.*)/)
		{
			print SEGCOMPARE "\n";
			$seqname1 = $1;
			$laterhalf1 = $2;
			print SEGCOMPARE "$seqname1$laterhalf1 \n";
		}
		elsif (m/^($seqname1)(.*)/)
		{
			#store the match sequence
			print SEGCOMPARE "$2 \n";
		}
	}
	my @segcomp = <SEGCOMPARE>;
#$count++;
#$temp++;
}
close(COMPARE);
close(SEGCOMPARE);
close(QUERRY);