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 get_gene_ids_of_transcript_id(transcript_id: str,
ensembl: pyensembl.Genome,
raise_on_error: bool = False):
""" Extract all gene ids associated with the given transcript.
Parameters
----------
transcript_id: string
The transcript identifier
ensembl: pyensembl.Genome
The annotations
raise_on_error: bool
Whether to raise an exception if the transcript id is not found in the
annotations database
Returns
-------
transcript_gene_id_df: pd.DataFrame
A dataframe with columns to map between transcripts and genes. Its
columns are:
transcript_id
gene_id
"""
try:
gene_name = ensembl.gene_name_of_transcript_id(transcript_id)
gene_ids = ensembl.gene_ids_of_gene_name(gene_name)
except ValueError as ve:
msg = ("['pyensembl_utils.get_gene_ids_of_transcript_id]: could not "
"find transcript id in database: {}".format(transcript_id))
if raise_on_error:
raise ValueError(msg) from ve
else:
logger.warning(msg)
return None
ret = [{'transcript_id': transcript_id, 'gene_id': g} for g in gene_ids]
return ret
