#!/usr/bin/perl use warnings; use strict; use diagnostics; my $file=$ARGV[0]; open (FILE,$file); while() { my @query=$_; foreach my $a (@query) { next until $a=~/^Query=.*$/; if($a=~/^Query=\s([^\s]+)\s.*$/) { print "$1\t"; next until $a=~/^>.+$/; if($a=~/^>([^\s]+)\s.*$/) { print "$1\n"; } } } }