def test_check_ensembl_id(): with TemporaryDirectory() as tmpdir: seqs = SequenceData([FASTA_PATH], require_ensembl_ids=True, cache_directory_path=tmpdir) with assert_raises(ValueError): seqs.get("WeirdID")
def test_check_ensembl_id(): with TemporaryDirectory() as tmpdir: seqs = SequenceData( FASTA_PATH, require_ensembl_ids=True, cache_directory_path=tmpdir) with assert_raises(ValueError): seqs.get("WeirdID")
def test_sequence_type(): with TemporaryDirectory() as tmpdir: seqs_dna = SequenceData(FASTA_PATH, sequence_type=DNA, cache_directory_path=tmpdir) seq = seqs_dna.get("ENSMUST00000138942") assert isinstance(seq, DNA) with TemporaryDirectory() as tmpdir: seqs_str = SequenceData(FASTA_PATH, sequence_type=str, cache_directory_path=tmpdir) seq = seqs_str.get("ENSMUST00000138942") assert isinstance(seq, str)
def test_sequence_type(): with TemporaryDirectory() as tmpdir: seqs_dna = SequenceData([FASTA_PATH], cache_directory_path=tmpdir) seq = seqs_dna.get("ENSMUST00000138942") assert seq is not None, \ "Failed to find sequence for ENSMUST00000138942" assert isinstance(seq, str), \ "Wrong sequence type, expected %s but got %s" % (str, type(seq))
def test_sequence_type(): with TemporaryDirectory() as tmpdir: seqs_dna = SequenceData( FASTA_PATH, cache_directory_path=tmpdir) seq = seqs_dna.get("ENSMUST00000138942") assert seq is not None, \ "Failed to find sequence for ENSMUST00000138942" assert isinstance(seq, str), \ "Wrong sequence type, expected %s but got %s" % (str, type(seq))
def test_missing_sequence(): with TemporaryDirectory() as tmpdir: seqs = SequenceData([FASTA_PATH], cache_directory_path=tmpdir) seq = seqs.get("NotInFasta") assert seq is None, "Should get None back for missing sequence"
def test_missing_sequence(): with TemporaryDirectory() as tmpdir: seqs = SequenceData(FASTA_PATH, cache_directory_path=tmpdir) seq = seqs.get("NotInFasta") assert seq is None, "Should get None back for missing sequence"