# List of headers
# BLAST file
# Output file (BLAST format)

use strict;

# Specify I/O

my $headerfile = $ARGV[0];
my $blastfile = $ARGV[1];
my $outfile = $ARGV[2];


# open header file
open (HEADERFILE, $headerfile) or die "Cannot open header file\n";
# open blast file
open (BLASTFILE, $blastfile) or die "Cannot open BLAST file\n";
# open output file
open(OUTPUT, ">$outfile");

my $ender = "Query=";

while (my $headerline = <HEADERFILE> ) {
	chomp $headerline;
	my $headercut = substr $headerline, 1;
	
	while (my $blastline = <BLASTFILE>) { 
		if ($blastline =~ $headercut) {
			print $blastline;
			print OUTPUT $blastline;
			print until ( ($_ = <BLASTFILE>) =~ /$ender/i);
			print OUTPUT until ( ($_ = <BLASTFILE>) =~ /$ender/i);
			}
			}
		seek (BLASTFILE,0,0);
		}
	

exit;