Python Genome.protein_sequence Beispiele

Beispiel #1

Datei: test_missing_genome_sources.py Projekt: yech1990/pyensembl

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)

Beispiel #2

Datei: test_missing_genome_sources.py Projekt: BioInfoTools/pyensembl

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)

Beispiel #3

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)

Beispiel #4

Datei: test_missing_genome_sources.py Projekt: BioInfoTools/pyensembl

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)