# This is part of the parser for Pfam data 


while($line=<IN>){
	chomp($line);
	if($line=~/^ID\s+(\w+)\s+/){
		$ID = $1;
	}
	elsif( $line=~/^OS\s+([\w\s]+)\s*\W/ ){
		$OS = $1 ;
		$OS =~s/\s+$// ;
	}
	if(($line=~/^\/\//) and ($OS eq $organism) ){
		$hash{$ID} = 1 ;
	}
}

print OUT
"Swiss_AC\tSwiss_ID\tPF_domain\tdomain_name\tdomain_description\tdomain_start\tdomain_end\n";
while($line=<DATA>){
	if($line=~/>([\w_]+)\s.*==\|\s+(\w+)\.\d+\s+(\d+)\s+a/){
		$protein= "$1\t$2\t";	
		$ID = $1 ;	
		if( $hash{$ID}==1 ){
		    do{
		    	$line=<DATA> ;
		    	chomp($line);
		    	if($line=~/(\w+)\s+.*(PF\d+)\.\d+\s+(\S.*\S)\s\s(\d+.*)/){
		    		$pfam="$2\t$1\t$3\t";
		    		@temp=split(/\s+/,$4 );
		    		foreach $temp(@temp){
		    			@position=split(/\-/,$temp);		    			
		    			print  OUT "$protein$pfam$position[0]\t$position[1]\n";		    			    
        
		    		}
		    	}
		    }until($line eq "");
	   }
	}
}

close IN ;
close DATA;
close OUT;