#!/usr/bin/perl -w
#usage: ./matchMF_HCgss.pl MFgss MF_match > MF_match.fsa

my %SEQ;


$/ = '>';
open(FILE, "$ARGV[0]") || die("Cannot open");
while(<FILE>){
	next unless /\w/;
	my @lines = split(/\n/, $_);
	my ($gi) = $lines[0] =~ /gi\|(\d+)/;
	shift @lines;
	my $seq = join('', @lines);
	$seq =~ s/\W+//g;
	$SEQ{$gi} = $seq;
}
close(FILE);
$/ = "\n";

my %ID;
open(FILE, "$ARGV[1]") || die("Canot open");
while(<FILE>){
	my ($gi) = /gi\|(\d+)/;
	next unless (defined $gi);
	next if(exists $ID{$gi});
	$ID{$gi} = 1;
	print ">$gi\n$SEQ{$gi}\n";
}
close(FILE);