def build_mgi_ensembl_map():
"""
@return: A bidirectional-map between MGI identifiers and Ensembl identifiers.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(mrk_ensembl_filename, "r"), delimiter='\t')
result = cookbook.BidirectionalMap()
for row in reader:
result.add(DbRef.parse_as(row[0], db.mgi), DbRef.parse_as(row[5], db.ensembl))
return result
def build_mgi_ensembl_map():
"""
@return: A bidirectional-map between MGI identifiers and Ensembl identifiers.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(mrk_ensembl_filename, "r"), delimiter='\t')
result = cookbook.BidirectionalMap()
for row in reader:
result.add(DbRef.parse_as(row[0], db.mgi),
DbRef.parse_as(row[5], db.ensembl))
return result
def build_mgi_name_map():
"""
@return: A map between MGI identifiers and marker names.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(mrk_ensembl_filename, "r"), delimiter='\t')
return dict((DbRef.parse_as(row[0], db.mgi), row[1]) for row in reader)
def build_mgi_name_map():
"""
@return: A map between MGI identifiers and marker names.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(mrk_ensembl_filename, "r"), delimiter='\t')
return dict(
(DbRef.parse_as(row[0], db.mgi), row[1])
for row
in reader
)
def build_mgi_go_map():
"""
@return: A map between MGI identifiers and GO ontologies.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(gene_association_filename, "r"), delimiter='\t')
result = cookbook.DictOfSets()
for row in reader:
if row[0].startswith('!'):
continue
result[DbRef.parse_as(row[1], db.mgi)].add(row[4])
return result
def build_mgi_go_map():
"""
@return: A map between MGI identifiers and GO ontologies.
"""
import csv, cookbook
from biopsy import DbRef, db
reader = csv.reader(open(gene_association_filename, "r"), delimiter='\t')
result = cookbook.DictOfSets()
for row in reader:
if row[0].startswith('!'):
continue
result[DbRef.parse_as(row[1], db.mgi)].add(row[4])
return result