|
1
|
|
|
#!/usr/bin/env python |
|
2
|
|
|
"""Test the loading of all optional GO term attributes. |
|
3
|
|
|
|
|
4
|
|
|
Maximum number of fields on a GO term: |
|
5
|
|
|
|
|
6
|
|
|
required: |
|
7
|
|
|
1 name |
|
8
|
|
|
1 namespace |
|
9
|
|
|
10 is_a |
|
10
|
|
|
16 alt_id |
|
11
|
|
|
|
|
12
|
|
|
optional scalar: |
|
13
|
|
|
1 def |
|
14
|
|
|
1 comment |
|
15
|
|
|
|
|
16
|
|
|
optional set: |
|
17
|
|
|
12 subset goslim_mouse |
|
18
|
|
|
|
|
19
|
|
|
optional special: |
|
20
|
|
|
3 relationship |
|
21
|
|
|
284 synonym synonym: "peptidase inhibitor complex" EXACT [GOC:bf, GOC:pr] |
|
22
|
|
|
827 xref Wikipedia:Zygotene |
|
23
|
|
|
|
|
24
|
|
|
|
|
25
|
|
|
In go-basic.obo fmt(1.2) rel(2018-02-11) 15,329 out of 47,120 GO Terms have synonym types: |
|
26
|
|
|
90444 EXACT |
|
27
|
|
|
18574 NARROW |
|
28
|
|
|
15037 RELATED |
|
29
|
|
|
3562 BROAD |
|
30
|
|
|
""" |
|
31
|
|
|
|
|
32
|
|
|
from __future__ import print_function |
|
33
|
|
|
|
|
34
|
|
|
import sys |
|
35
|
|
|
from goatools.test_data.optional_attrs import OptionalAttrs |
|
36
|
|
|
|
|
37
|
|
|
|
|
38
|
|
|
def test_optional_attrs(): |
|
39
|
|
|
"""Test loading optional GO term field, 'synonym'.""" |
|
40
|
|
|
prt = sys.stdout |
|
41
|
|
|
prt = None |
|
42
|
|
|
# Summary for all fields in a GO DAG |
|
43
|
|
|
opt_attrs = ['def', 'comment', 'subset', 'synonym', 'xref', 'relationship'] |
|
44
|
|
|
obj = OptionalAttrs("go-basic.obo", opt_attrs) |
|
45
|
|
|
obj.prt_summary() |
|
46
|
|
|
|
|
47
|
|
|
# SCALAR: Check optional attributes whose information is stored in string |
|
48
|
|
|
for attr in ['defn', 'comment']: |
|
49
|
|
|
# Check that all GOTerms have a string; ACTUAL matches EXPECTED if present, else "" |
|
50
|
|
|
obj.chk_str(attr) |
|
51
|
|
|
print("PASSED COUNT TEST: {ATTR}".format(ATTR=attr)) |
|
52
|
|
|
|
|
53
|
|
|
# SET: Check optional attributes whose information is stored in a set |
|
54
|
|
|
# Check that all GO IDs that should have relationships do have relationships. |
|
55
|
|
|
# For each GO ID, check that actual count of a set attr equals expected count |
|
56
|
|
|
obj.chk_set('subset') |
|
57
|
|
|
print("PASSED: subset") |
|
58
|
|
|
|
|
59
|
|
|
# RELATIONSHIP: Stored in a dict with values being sets of GO IDs |
|
60
|
|
|
obj.chk_relationships() |
|
61
|
|
|
print("PASSED: relationship") |
|
62
|
|
|
|
|
63
|
|
|
# SYNONYM: Synonyms are stored in a list of namedtuples |
|
64
|
|
|
obj.chk_synonyms(prt) |
|
65
|
|
|
print("PASSED: synonyms") |
|
66
|
|
|
|
|
67
|
|
|
# XREF: Stored in a set |
|
68
|
|
|
obj.chk_xref(prt) |
|
69
|
|
|
print("PASSED: xrefs") |
|
70
|
|
|
|
|
71
|
|
|
def test_no_optional_attrs(): |
|
72
|
|
|
"""Test loading DAG with no optional attributes.""" |
|
73
|
|
|
obj = OptionalAttrs("go-basic.obo", None) |
|
74
|
|
|
obj.chk_no_optattrs() |
|
75
|
|
|
obj = OptionalAttrs("go-basic.obo", []) |
|
76
|
|
|
obj.chk_no_optattrs() |
|
77
|
|
|
obj = OptionalAttrs("go-basic.obo", set([])) |
|
78
|
|
|
obj.chk_no_optattrs() |
|
79
|
|
|
|
|
80
|
|
|
|
|
81
|
|
|
if __name__ == '__main__': |
|
82
|
|
|
test_no_optional_attrs() |
|
83
|
|
|
test_optional_attrs() |
|
84
|
|
|
|
|
85
|
|
|
# Copyright (C) 2010-2018, H Tang et al., All rights reserved. |
|
86
|
|
|
|
tanghaibao /
goatools
