def test_dna_fasta_format_invalid_characters(self):
filepath = self.get_data_path('not-dna-sequences.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, "Invalid character '1' "
".*0 on line 2"):
format.validate()
def test_dna_fasta_format_id_starts_with_space(self):
filepath = self.get_data_path(
'dna-sequences-id-starts-with-space.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, '1 starts with a space'):
format.validate()
def test_dna_fasta_format_consecutive_IDs(self):
filepath = self.get_data_path('dna-sequences-consecutive-ids.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(
ValidationError, 'consecutive descriptions.*1'):
format.validate()
def test_dna_fasta_format_empty_file(self):
filepath = os.path.join(self.temp_dir.name, 'empty')
with open(filepath, 'w') as fh:
fh.write('\n')
format = DNAFASTAFormat(filepath, mode='r')
format.validate()
def test_dna_fasta_format_empty_file(self):
filepath = os.path.join(self.temp_dir.name, 'empty')
with open(filepath, 'w') as fh:
fh.write('\n')
format = DNAFASTAFormat(filepath, mode='r')
format.validate()
def test_dna_fasta_format_validate_negative(self):
filepath = self.get_data_path('not-dna-sequences')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValueError, 'DNAFASTA'):
format.validate()
def test_dna_fasta_format_validate_positive(self):
filepath = self.get_data_path('dna-sequences.fasta')
format = DNAFASTAFormat(filepath, mode='r')
format.validate()
def test_dna_fasta_format_no_id(self):
filepath = self.get_data_path('dna-sequences-no-id.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, '1.*missing an ID'):
format.validate()
def test_dna_fasta_format_duplicate_ids(self):
filepath = self.get_data_path('dna-sequences-duplicate-id.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, '3.*duplicate.*1'):
format.validate()
def test_dna_fasta_format_bom_fails(self):
filepath = self.get_data_path('dna-with-bom-fails.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'First line'):
format.validate()
def test_dna_fasta_format_corrupt_characters(self):
filepath = self.get_data_path('dna-sequences-corrupt-characters.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'utf-8.*2'):
format.validate()
def test_dna_fasta_format_missing_initial_ID(self):
filepath = self.get_data_path('dna-sequences-first-line-not-id.fasta')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'First line'):
format.validate()
def test_dna_fasta_format_validate_negative(self):
filepath = self.get_data_path('not-dna-sequences')
format = DNAFASTAFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'DNAFASTA'):
format.validate()
def test_dna_fasta_format_bom_passes(self):
filepath = self.get_data_path('dna-with-bom-passes.fasta')
format = DNAFASTAFormat(filepath, mode='r')
format.validate()
def test_dna_fasta_format_validate_positive(self):
filepath = self.get_data_path('dna-sequences.fasta')
format = DNAFASTAFormat(filepath, mode='r')
format.validate()
