#!/usr/bin/perl -w
#################################################
### Huang He                               		###
### 2012/04/18                           	 		###
### take_out_special_sequnces_from_fasta_file ###
#################################################
($blastn_best,$fasta)=@ARGV;
open(File,"$blastn_best")||die "can't open the $blastn_best\n";
while(<File>){
chomp;
s/\c@*//g;
s/\cM*$//;
	@temp=split;
	$bnm=">$temp[0]";
	$id{$bnm}=0;
}
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;
		if(! exists $id{$line}){
			$flag=0;
		}
	}
	if($flag==0){
		print"$line\n";
	}
}
close File;