def test_transcript_fasta_only(): genome = Genome(reference_name="GRCm38", annotation_name="_test_mouse_ensembl81_subset", transcript_fasta_paths_or_urls=[ MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH ]) genome.index() eq_(2, len(genome.transcript_sequences.fasta_dictionary)) with assert_raises(ValueError) as cm: genome.genes() no_gtf_(cm) with assert_raises(ValueError) as cm: genome.gene_ids() no_gtf_(cm) with assert_raises(ValueError) as cm: genome.gene_ids_of_gene_name("test") no_gtf_(cm) with assert_raises(ValueError) as cm: genome.transcript_names() no_gtf_(cm) with assert_raises(ValueError) as cm: genome.protein_sequence("test") no_protein_(cm)
def test_transcript_fasta_only(): genome = Genome( reference_name="GRCm38", annotation_name="_test_mouse_ensembl81_subset", transcript_fasta_path_or_url=MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH) genome.index() eq_(2, len(genome.transcript_sequences.fasta_dictionary)) with assert_raises(ValueError) as cm: genome.genes() no_gtf_(cm) with assert_raises(ValueError) as cm: genome.gene_ids() no_gtf_(cm) with assert_raises(ValueError) as cm: genome.gene_ids_of_gene_name("test") no_gtf_(cm) with assert_raises(ValueError) as cm: genome.transcript_names() no_gtf_(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_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)