def get_gene_name_of_transcript_id(transcript_id: str,
ensembl: pyensembl.Genome,
raise_on_error: bool = False):
""" Extract the gene name (symbol) for this transcript id.
The difference between this function and gene_name_of_transcript_id is that
this function will (optionally) issue a warning rather than raise an
exception for transcript ids not in the database.
Parameters
----------
transcript_id: string
The transcript identifier (e.g., "ENSMUST00000035194")
ensembl: pyensembl.Genome
The annotation database
raise_on_error: bool
Whether to issue a warning (False) or raise a ValueError (True) if the
transcript identifier is not in the annotation database
Returns
-------
gene_name: string
The gene name (also called gene symbol, e.g., "Mapkapk3")
--- OR ---
None, if the transcript id is not in the database of annotations
"""
gene_name = None
try:
gene_name = ensembl.gene_name_of_transcript_id(transcript_id)
except ValueError as ve:
msg = ("[pyensembl_utils.get_gene_name_of_transcript_id]: could not "
"find match for transcript id: {}".format(transcript_id))
if raise_on_error:
raise ValueError(msg) from ve
else:
logger.warning(msg)
return gene_name
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