def test_gtf_only():
genome = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH)
genome.index()
eq_(1, len(genome.genes()))
with assert_raises(ValueError) as cm:
genome.transcript_sequence("test")
no_transcript_(cm)
with assert_raises(ValueError) as cm:
genome.protein_sequence("test")
no_protein_(cm)
def test_gtf_only():
genome = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH)
genome.index()
eq_(1, len(genome.genes()))
with assert_raises(ValueError) as cm:
genome.transcript_sequence("test")
no_transcript_(cm)
with assert_raises(ValueError) as cm:
genome.protein_sequence("test")
no_protein_(cm)
def test_protein_fasta_only():
genome_only_proteins = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
protein_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH])
genome_only_proteins.index()
eq_(4, len(genome_only_proteins.protein_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome_only_proteins.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome_only_proteins.transcript_sequence("DOES_NOT_EXIST")
no_transcript_(cm)
def test_protein_fasta_only():
genome = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
protein_fasta_paths_or_urls=[
MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH
])
genome.index()
eq_(4, len(genome.protein_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.transcript_sequence("test")
no_transcript_(cm)