for c in chr_list:
chrQuery = {'chr': c}
updateDict = {'CHR': ''.join(['chr', c])}
setDict = {'$set': updateDict}
print 'Adding chr prefix for CHR fields containing %s' % (c)
mongo.update(collection_name, chrQuery, setDict)
distinct = mongo.distinct(collection_name, 'chr')
print 'chromosomes updated to:'
print distinct
print 'Done in %i seconds' % (time.time() - starttime)
if __name__ == "__main__":
annotation_name = 'annotations'
p = Parameters.parameter()
mongo = Mongo_Connector.MongoConnector(p.get('server'), p.get('port'), p.get('default_database'))
# mongo.ensure_index(annotation_name, 'chr') # don't index just on chromosome name
chromosome_list = [str(i) for i in range(1, 22)] # Create an expected list of chromosomes
chromosome_list.append('X')
chromosome_list.append('Y')
print 'Adding prefix chr to chromosome field in methyl450 arrays...'
AddChrPrefix(annotation_name, chromosome_list)
mongo.close()
sys.path.insert(0, _root_dir + os.sep + "CommonUtils")
import Parameters
import Mongo_Connector
def gene_to_lower():
'''append chr prefix.'''
starttime = time.time()
cursor = mongodb.find('ensgenes', {}, {"name":1, "_id":0})
for gene in cursor:
# print "gene.name = %s" % (gene['name'])
mongodb.update('ensgenes', {"name":gene['name']}, {'$set': {'namelc':gene['name'].lower()}})
print 'Done in %i seconds' % (time.time() - starttime)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
# parser.add_argument("csvbeta", help = "The file name of the CSV beta file to import", type = str)
parser.add_argument("-dbconfig", help = "An optional file to specify the database location - default is database.conf in MongoDB directory", type = str, default = None)
parser.add_argument("-dbname", help = "name of the Database in the Mongo implementation to use - default is provided in the database.conf file specified", type = str, default = None)
args = parser.parse_args()
p = Parameters.parameter(args.dbconfig)
if args.dbname:
p.set("default_database", args.dbname)
mongodb = Mongo_Connector.MongoConnector(p.get('server'), p.get('port'), p.get('default_database'))
gene_to_lower()
mongodb.close()