# Test psp-gen on DNA
&test(
  'psp-gen1', 
  'DNA sequences',
  'psp-gen', 
  '',
  [
    '-revcomp', 
    '-pos', make_test_src_path('psp-gen/one-peak-dna.fasta'), 
    '-neg', make_test_src_path('psp-gen/all-A.fasta')
  ],
  [
    {
        output => '-', 
        reference => make_test_src_path('psp-gen/one-peak-dna-revcomp.psp'), 
        type => 'text'
    }
  ],
  'results/pspgen1', 'scripts'
);

# Test psp-gen on protein
&test(
  'psp-gen2', 
  'protein sequences',
  'psp-gen', 
  '',
  [
    '-protein', 
    '-maxrange', 
    '-triples', 
    '-pos', make_test_src_path('psp-gen/one-peak-protein.fasta'),
    '-neg', make_test_src_path('psp-gen/all-A.fasta')
  ],
  [
    {
      output => '-', 
      reference => make_test_src_path('psp-gen/one-peak-protein.psp'), 
      type => 'text'
    }
  ],
  'results/pspgen2', 'scripts'
);

# Test psp-gen on DNA, using an expanded alphabet which contains the
# conventional DNA alphabet as a subset.
# The input is the same as the normal DNA test and the alphabet is a superset,
# so the output should be identical.
&test(
  'psp-gen3', 
  'conventional DNA sequences with an expanded alphabet',
  'psp-gen', 
  '',
  [
    '-alph', 'common/extended_dna.alph', 
    '-revcomp', 
    '-pos', make_test_src_path('psp-gen/one-peak-dna.fasta'), 
    '-neg', make_test_src_path('psp-gen/all-A.fasta')
  ],
  [
    {
      output => '-', 
      reference => make_test_src_path('psp-gen/one-peak-dna-revcomp.psp'), 
      type => 'text'
    }
  ],
  'results/pspgen1', 'scripts'
);

