def __init__(self, rs_id_file):
'''
:param rs_id_file: str
:param output_tsv_file: str
:return: None
'''
self.assigned_variants = AssignVariants(rs_id_file)
self.tsv_file_header = ['rs_id',
'in_ensembl',
'ensembl_gene_ids',
'gene_symbols',
'so_term',
'distance']
self.output_rows = self.__process_assigned_variants()
self.reference_gene_map = self.__get_reference_gene_map()
class WriteGeneAssignments:
def __init__(self, rs_id_file):
'''
:param rs_id_file: str
:param output_tsv_file: str
:return: None
'''
self.assigned_variants = AssignVariants(rs_id_file)
self.tsv_file_header = ['rs_id',
'in_ensembl',
'ensembl_gene_ids',
'gene_symbols',
'so_term',
'distance']
self.output_rows = self.__process_assigned_variants()
self.reference_gene_map = self.__get_reference_gene_map()
def __process_assigned_variants(self):
'''
:return: list
'''
assigned_variant_list = self.assigned_variants.get_assigned_variant_list()
output_rows = []
for row_map in assigned_variant_list:
rs_id = row_map['variant_id']
in_ensembl = row_map['is_in_ensembl?']
if row_map['vep_associated_gene_ids']:
so_term = row_map['most_severe_consequence']
distance = 0
ensembl_gene_ids = row_map['vep_associated_gene_ids']
elif row_map['most_severe_consequence'] == 'regulatory_region_variant':
so_term = 'nearest_gene_five_prime_end_reg'
distance = row_map['nearest_ensembl_5p_distance']
ensembl_gene_ids = [row_map['nearest_5p_ensembl_gene_id']]
else:
so_term = 'nearest_gene_five_prime_end'
distance = row_map['nearest_ensembl_5p_distance']
ensembl_gene_ids = [row_map['nearest_5p_ensembl_gene_id']]
output_rows.append([rs_id, in_ensembl, ensembl_gene_ids,so_term, distance ])
return output_rows
def __get_reference_gene_map(self):
'''
:return: dict
'''
ensembl_gene_ids = []
for output_row in self.output_rows:
ensembl_gene_ids.extend(output_row[2])
ensembl_id_uniq = list(set(ensembl_gene_ids))
exec_ensembl_perl = ExecuteEnsemblPerl()
reference_gene_map = exec_ensembl_perl.get_ensembl_gene_id_ref_map(ensembl_id_uniq)
return reference_gene_map
def write_output_to_file(self, path_to_output_file):
'''
:param path_to_file: string
:return: None
'''
new_output_rows = []
for output_row in self.output_rows:
(rs_id, in_ensembl, ensembl_gene_ids, so_term, distance) = output_row
# (output_row[0], output_row[1], output_row[2], output_row[3])
gene_symbols = []
ensembl_gene_id_references = []
for ensembl_gene_id in ensembl_gene_ids:
try:
ref_gene_map = self.reference_gene_map[ensembl_gene_id]
except KeyError:
continue
gene_symbol = ref_gene_map['external_name']
ensembl_gene_id_reference = ref_gene_map.get('ensembl_gene_id_for_reference', None)
gene_symbols.append(gene_symbol)
ensembl_gene_id_references.append(ensembl_gene_id_reference)
new_output_row = [rs_id, in_ensembl, ','.join(ensembl_gene_id_references), ','.join(gene_symbols), so_term, distance]
new_output_rows.append(new_output_row)
with open(path_to_output_file, 'w') as fho:
for data_row in new_output_rows:
fho.write('\t'.join([str(element) for element in data_row]) + '\n')