1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
import MySQLdb
import re
import configparser
def get_cursor():
host = 'tux.uthsc.edu'
user = 'webqtlout'
passwd = 'webqtlout'
db = 'db_webqtl'
con = MySQLdb.Connect(db=db, host=host, user=user, passwd=passwd)
cursor = con.cursor()
return cursor, con
def clearspaces(s, default=None):
if s:
s = re.sub('\s+', ' ', s)
s = s.strip()
return s
else:
return default
def to_dic(keys, values):
dic = {}
for i in range(len(keys)):
key = keys[i]
value = values[i]
dic[key] = value
return dic
def overlap(dic1, dic2):
keys = []
values1 = []
values2 = []
for key in dic1.keys():
if key in dic2:
value1 = dic1[key]
value2 = dic2[key]
if value1 and value2:
keys.append(key)
values1.append(value1)
values2.append(value2)
return keys, values1, values2
def to_db_string(s, default):
if s:
s = s.strip()
if len(s) == 0:
return default
elif s == 'x':
return default
else:
return s
else:
return default
def to_db_float(s, default):
if s:
s = s.strip()
if len(s) == 0:
return default
elif s == 'x':
return default
else:
try:
return float(s)
except:
return default
else:
return default
def to_db_int(s, default):
if s:
s = s.strip()
if len(s) == 0:
return default
elif s == 'x':
return default
else:
try:
return int(s)
except:
return default
else:
return default
def get_config(configfile):
config = configparser.ConfigParser()
config.read(configfile)
return config
|
