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()