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
|
from __future__ import print_function, division
import re
from pprint import pformat as pf
def parse(pstring):
pstring = re.split(r"""(?:(\w+\s*=\s*\([^)]*\))|(\w+\s*[=:]\w+)|(\w+))""", pstring)
pstring = [item.strip() for item in pstring if item and item.strip()]
print(pstring)
items = []
for item in pstring:
if ":" in item:
key, seperator, value = item.partition(':')
elif "=" in item:
key, seperator, value = item.partition('=')
else:
seperator = None
if seperator:
if '(' in value:
assert value.startswith("("), "Invalid token"
assert value.endswith(")"), "Invalid token"
value = value[1:-1] # Get rid of the parenthesis
values = re.split(r"""\s+|,""", value)
value = [value.strip() for value in values if value.strip()]
# Brackets can also be used to encapsulate values
elif '[' in value:
assert value.startswith("["), "Invalid token"
assert value.endswith("]"), "Invalid token"
value = value[1:-1] # Get rid of the brackets
values = re.split(r"""\s+|,""", value)
value = [value.strip() for value in values if value.strip()]
term = dict(key=key,
seperator=seperator,
search_term=value)
else:
term = dict(key=None,
seperator=None,
search_term = item)
items.append(term)
print(pf(items))
return(items)
if __name__ == '__main__':
parse("foo=(3 2 1)")
parse("shh")
parse("shh grep")
parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)")
parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)")
parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)")
parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
|
