def get_all_ids(attr_path, biotype=None, filter_set=set(), id_type="Transcript"):
"""
returns the set of ensembl IDs in the entire Gencode database pulled from the attribute
"""
assert id_type in ["Transcript", "Gene"]
if id_type == "Transcript":
if biotype is None:
return {x.split()[3] for x in skip_header(attr_path) if x not in filter_set}
else:
return {x.split()[3] for x in skip_header(attr_path) if x.split()[4] == biotype if x not in filter_set}
else:
if biotype is None:
return {x.split()[0] for x in skip_header(attr_path) if x not in filter_set}
else:
return {x.split()[0] for x in skip_header(attr_path) if x.split()[4] == biotype if x not in filter_set}
def get_gene_map(attr_path):
"""
Returns a dictionary mapping all transcript IDs to their respective gene IDs
"""
return {x.split()[3]: x.split()[0] for x in skip_header(attr_path)}
def get_all_biotypes(attr_path):
"""
Returns all biotypes in the attribute database.
"""
return {x.split()[4] for x in skip_header(attr_path)}
def get_gene_biotype_map(attr_path):
"""
Returns a dictionary mapping all gene IDs to their respective biotypes
"""
return {x.split()[0]: x.split()[2] for x in skip_header(attr_path)}
