#!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 $librar
+y");
if ($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 o
+ff
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 "$2 \n";
                }
                if(m/>>/)
                {
                    #check if next sequence if so rewind one line back
+";                
                    seek(FASTA,-100,1);
                    #break command
                    last;
                 }
            }
            print INPUT "\n";
            print ORG "\n";
            close(INPUT);
            close(ORG);
        }
        else
        {
            #printing all the sequences which is showed in fasta o/p f
+ile
            open(ORG,">>$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);
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