my $verbose = 1;
my @controls = ('no', 'yes');
my $primary_only = 'common/Klf1-200-100.combined.fa';
my $primary = 'common/Klf1-200-100.fa';
my $control = 'common/Klf1-200-100-shuffled.py2.fa';
my @motifs = ('common/Jaspar-subset.meme', 'common/Jaspar-subset2.meme');

my $counter = 1;
foreach my $cntrl (@controls) {
  my @args = ();
  my $cntrl_str;
  if ($cntrl eq 'yes') {
    $cntrl_str = 'control';
    push(@args, '--p', $primary);
    push(@args, '--n', $control);
    push(@args, '--motif-pseudo', '0', '--hofract', '0');
  } elsif ($cntrl eq 'no') {
    $cntrl_str = 'no_control';
    push(@args, '--p', $primary_only);
    push(@args, '--bfile', '--uniform--') if ($counter != 1);
  }
  if ($counter == 1) {
    push(@args, '--m', "'$motifs[0]'");
    push(@args, '--thresh', '0.1', '--qvalue');
  } else {
    foreach my $motif (@motifs) {
      push(@args, '--m', "'$motif'");
    }
    push(@args, '--thresh', '10');
  }
  my $out = 'sea.'.$cntrl_str;
  my $check_html =
    {
      output => 'results/sea'.$counter.'/sea.html',
      reference => make_test_src_path('sea/'.$out.'.html'),
      type => 'json', ignore => [
	'data:(version|revision|release|cmd)'
      ]
    };
  my $check_tsv =
    {
      output => 'results/sea'.$counter.'/sea.tsv', 
      reference => make_test_src_path('sea/'.$out.'.tsv'),
      type => 'text', ignore => ['^#']
    };
  my $check_seq = 
    {
      output => 'results/sea'.$counter.'/sequences.tsv', 
      reference => make_test_src_path('sea/'.$out.'.sequences.tsv'),
      type => 'text', ignore => ['^#']
    };

  &test('sea'.$counter, '',
    'sea', '',
    ['--verbosity', $verbose, '--oc', 'results/sea'.$counter, @args
    ],
    [$check_html, $check_tsv, $check_seq],
    catdir('results', 'sea' . $counter)
  );
  $counter++;
} # control

$out = "dna_with_covalent";
&test('sea'.$counter, '--xalph, --inc, --exc, --bfile, --order, --motif-pseudo',
  'sea', '',
  ['--oc', 'results/sea'.$counter, '--verbosity', 1,
    '--xalph', 'common/'.$out.'.alph',
    '--inc', 'MA00*', '--inc', 'MA04*', '--exc', 'MA007*', '--inc', 'T*',
    '--bfile', 'common/dna_with_covalent.bg', '--order', '0',
    '--qvalue',
    '--p', 'common/dna_with_covalent.fa', '--m', 'common/Jaspar-subset.meme',
    '--m', 'common/Jaspar-subset2.meme', '--m', 'common/dna_with_covalent.meme'
  ],
  [
    {
      output => 'results/sea'.$counter.'/sea.html',
      reference => make_test_src_path('sea/sea.'.$out.'.html'),
      type => 'json', ignore => [
	'data:(version|revision|release|cmd)',
	'data:sequence_db:source'
      ]
    },
    {
      output => 'results/sea'.$counter.'/sea.tsv',
      reference => make_test_src_path('sea/sea.'.$out.'.tsv'),
      type => 'text', ignore => ['^#']
    },
    {
      output => 'results/sea'.$counter.'/sequences.tsv', 
      reference => make_test_src_path('sea/sea.'.$out.'.sequences.tsv'),
      type => 'text', ignore => ['^#']
    }
  ],
  'results/sea'.$counter
);
$counter++;