use strict;
use warnings;

my @files = qw / NC_002755.fq NC_009525.fq NC_009565.fq NC_012943.fq NC_016768.fq NC_016934.fq NC_017026.fq NC_017522.fq NC_017523.fq NC_017524.fq NC_017528.fq NC_018078.fq NC_018143.fq NC_020089.fq /;
@files = map {s/\.fq$//; $_} @files;
while (my $seq = <DATA>) {
    my @seq = split /\s+/, $seq;
    printf "%-50s", "@seq[0..1] ";
    my %found_files = map { s/\.\w+$// ; $_ => 1} grep {/NC_/} @seq[2..$#seq];
    for my $file (@files) {
        print exists $found_files{$file} ? "1\t" : "0\t"
    }
    print "\n";
}

__DATA__
(3R)-hydroxyacyl-ACP dehydratase subunit HadA    NC_021192.1
(3R)-hydroxyacyl-ACP dehydratase subunit HadB    NC_017026.1
(dimethylallyl)adenosine tRNA methylthiotransferase    NC_009565.1    NC_002755.2    NC_009525.1    NC_016934.1
1,4-alpha-glucan branching protein    NC_021192.1    NC_017522.1    NC_016934.1    NC_018078.1    NC_020089.1    NC_002755.2    NC_017524.1    NC_009565.1    NC_012943.1    NC_017523.1    NC_021740.1
1,4-dihydroxy-2-naphthoate octaprenyltransferase    NC_016934.1    NC_017026.1    NC_009525.1
1,4-dihydroxy-2-naphthoyl-CoA synthase    NC_018143.2    NC_009565.1    NC_002755.2    NC_012943.1    NC_017523.1