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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
"""
DESCRIPTION:
TODO: Add a description for the module
FUNCTIONS:
slink:
TODO: Describe what the function does...
"""
from functools import partial
class LengthError(BaseException):
pass
class MirrorError(BaseException):
pass
def __is_list_or_tuple(item):
return type(item) in [list, tuple]
def __raise_valueerror_if_data_is_not_lists_or_tuples(lists):
"""Check that `lists` is a list of lists: If not, raise an exception."""
if (not __is_list_or_tuple(lists)) or (not all(map(__is_list_or_tuple, lists))):
raise ValueError("Expected list or tuple")
def __raise_valueerror_if_lists_empty(lists):
"""Check that the list and its direct children are not empty."""
def empty(lst):
return len(lst) == 0
if (empty(lists)) or not all(map(lambda x: not empty(x), lists)):
raise ValueError("List/Tuple should NOT be empty!")
def __raise_lengtherror_if_child_lists_are_not_same_as_parent(lists):
def len_is_same_as_parent(lst):
return len(lst) == len(lists)
if not all(map(len_is_same_as_parent, lists)):
raise LengthError("All children lists should be same length as the parent.")
def __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
def get_child_distance(child):
idx = lists.index(child)
return lists[idx][idx]
def distance_is_zero(dist):
return dist == 0
children_distances = map(get_child_distance, lists)
if not all(map(distance_is_zero, children_distances)):
raise ValueError("Distance of each child list/tuple from itself should be zero!")
def __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
"""Check that the distance from A to B, is the same as the distance from B to A.
If the two distances are different, throw an exception."""
for i in range(len(lists)):
for j in range(len(lists)):
if lists[i][j] != lists[j][i]:
raise MirrorError(
("Distance from one child({}) to the other ({}) "
"should be the same in both directions.").format(
lists[i][j], lists[j][i]))
def __raise_valueerror_on_negative_distances(lists):
"""Check that distances between 'somethings' are all positive, otherwise,
raise an exception."""
def zero_or_positive(val):
return val >= 0;
# flatten lists
flattened = [distance for child in lists for distance in child]
if not all(map(zero_or_positive, flattened)):
raise ValueError("Distances should be positive.")
def nearest(lists, i, j):
"""
Computes shortest distance between member(s) in `i` and member(s) in `j`.
Description:
This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
This description should be updated to better describe what 'member' means in
the context where the function is used.
Parameters:
lists (list of lists of distances): Represents a list of members and their
distances from each other.
Each inner list represents the distances the member at that coordinate
is from other members in the list: for example, a member at index 0 with
the values [0, 9, 1, 7] indicates that the member is:
- 0 units of distance away from itself
- 9 units of distance away from member at coordinate 1
- 1 unit of distance away from member at coordinate 2
- 7 units of distance away from member at coordinate 3
i (int or list of ints): Represents the coordinate of a member, or a list of
coordinates of members on the `lists` list.
j (int or list of ints): Represents the coordinate of a member, or a list of
coordinates of members on the `lists` list.
Returns:
int: Represents the shortest distance between member(s) in `i` and member(s)
in `j`."""
#### Guard Functions: Should we do this a different way? ####
__raise_valueerror_if_data_is_not_lists_or_tuples(lists)
__raise_valueerror_if_lists_empty(lists)
__raise_lengtherror_if_child_lists_are_not_same_as_parent(lists)
__raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists)
__raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
__raise_valueerror_on_negative_distances(lists)
#### END: Guard Functions ####
if type(i) == int and type(j) == int: # From member i to member j
return lists[i][j]
elif type(i) == int and __is_list_or_tuple(j):
return min(map(lambda j_new: nearest(lists, i, j_new), j))
elif type(j) == int and __is_list_or_tuple(i):
return min(map(lambda i_new: nearest(lists, i_new, j), i))
elif __is_list_or_tuple(i) and __is_list_or_tuple(j):
partial_i = map(lambda x:partial(nearest, lists, x), i[:-1])
ns = list(map(lambda f, x: f(x), partial_i, j[:1]))
return min(ns)
else:
raise ValueError("member values (i or j) should be lists/tuples of integers or integers")
|
