#!/usr/bin/perl -w
#######################################################################
### Huang He                                                        ###
### take fasta file from original fasta by blasted(unfinished) file ###
#######################################################################

($bwa,$fasta)=@ARGV;
open(File,"$bwa")||die "can't open the $bwa\n";
while(<File>){
chomp;
s/\c@*//g;
s/\cM*$//;
	if(/^\@SQ/){
		next;
	}
	@temp=split;
	if($temp[2] eq "*"){
		$id{$temp[0]}=0;
	}
#	print"$query\n";
}
close File;

open(File,"$fasta")||die "can't open the $fasta\n";
$flag=0;
while(<File>){
chomp;
s/\c@*//g;
s/\cM*$//;
	$line=$_;
	if(/^\>/){
		$flag=1;
		$line=~s/\>//g;
		if(! exists $id{$line}){ 
			$flag=0;
			next;
		}
		print">$line\n";
		next;
	}
	if($flag==0){
			next;
	}
	print"$line\n";
}
close File;