def get_genbank(self,
accession_number,
saveas,
host='interaction.cbs.dtu.dk',
user='',
passwd='',
database='genbank_xml'):
conn = MySQLdb.connnect(host, user, passwd, database)
curs = self.conn.cursor()
accession = accession_number.split('.', 1)
if (len(accession) == 1):
curs.execute("""SELECT uncompress(data_z) FROM raw_ff WHERE locus=?""",
(accession[0], ))
elif (len(accession) == 2):
curs.execute(
"""SELECT uncompress(data_z) FROM raw_ff WHERE locus=? AND version=?""",
(accession[0], int(accession[1])))
else:
return False
result = self.curs.fetchone()
if (result == None):
return False
decoded = str.decode(result[0])
o = open(saveas, 'wb')
o.write(decoded)
o.close()
conn.close()
return True
def get_genbank(self, accession_number, saveas, host='interaction.cbs.dtu.dk', user='', passwd='', database='genbank_xml'):
conn = MySQLdb.connnect(host, user, passwd, database)
curs = self.conn.cursor()
accession = accession_number.split('.',1)
if(len(accession)==1):
curs.execute("""SELECT uncompress(data_z) FROM raw_ff WHERE locus=?""", (accession[0],))
elif(len(accession)==2):
curs.execute("""SELECT uncompress(data_z) FROM raw_ff WHERE locus=? AND version=?""", (accession[0],int(accession[1])))
else:
return False
result = self.curs.fetchone()
if(result == None):
return False
decoded = str.decode(result[0])
o = open(saveas, 'wb')
o.write(decoded)
o.close()
conn.close()
return True
#!/usr/bin/python3
"""
Script that lists all states from the database hbtn_0e_0_usa.
"""
import MySQLdb
import sys
if __name__ == "__main__":
db = MySQLdb.connnect(host="localhost",
user=sys.argv[1],
port=3306,
password=sys.argv[2],
db=sys.argv[3])
cursor = db.cursor()
sql = "SELECT id, name FROM states ORDER BY id ASC"
cursor.execute(sql)
states = cursor.fetchall()
if states is not None:
for row in states:
print("({}, '{}')".format(row[0], row[1]))
cursor.close()
db.close()
