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elewis2elewis2
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format tests
1 parent 437bd8f commit 9eff4f0

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lines changed

‎tests/test_graphkb/data.py‎

Lines changed: 124 additions & 124 deletions
Original file line numberDiff line numberDiff line change
@@ -7,72 +7,72 @@
77
#
88
structuralVariants = {
99
# Unambiguous structural variations
10-
"(FGFR3,BRCA2):fusion(g.1234567,g.1234567)": {
11-
"matches": {
12-
"displayName": ["FGFR3 fusion", "FGFR3 rearrangement"],
13-
"type": ["fusion", "rearrangement"],
10+
'(FGFR3,BRCA2):fusion(g.1234567,g.1234567)': {
11+
'matches': {
12+
'displayName': ['FGFR3 fusion', 'FGFR3 rearrangement'],
13+
'type': ['fusion', 'rearrangement'],
1414
}
1515
},
1616
# ambiguous structural variations -> structural
17-
"FGFR3:c.1200_1300dup": {
18-
"matches": {
19-
"displayName": ["FGFR3 mutation", "FGFR3 rearrangement"],
20-
"type": ["mutation", "rearrangement"],
17+
'FGFR3:c.1200_1300dup': {
18+
'matches': {
19+
'displayName': ['FGFR3 mutation', 'FGFR3 rearrangement'],
20+
'type': ['mutation', 'rearrangement'],
2121
}
2222
},
23-
"FGFR3:c.1200_1201insACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT": {
24-
"matches": {
25-
"displayName": ["FGFR3 mutation", "FGFR3 rearrangement"],
26-
"type": ["mutation", "rearrangement"],
23+
'FGFR3:c.1200_1201insACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT': {
24+
'matches': {
25+
'displayName': ['FGFR3 mutation', 'FGFR3 rearrangement'],
26+
'type': ['mutation', 'rearrangement'],
2727
}
2828
},
29-
"FGFR3:g.5000_5100del": {
30-
"matches": {
31-
"displayName": ["FGFR3 mutation", "FGFR3 rearrangement"],
32-
"type": ["mutation", "rearrangement"],
29+
'FGFR3:g.5000_5100del': {
30+
'matches': {
31+
'displayName': ['FGFR3 mutation', 'FGFR3 rearrangement'],
32+
'type': ['mutation', 'rearrangement'],
3333
}
3434
},
35-
"FGFR3:c.1200_1300delinsA": {
36-
"matches": {
37-
"displayName": ["FGFR3 mutation", "FGFR3 rearrangement"],
38-
"type": ["mutation", "rearrangement"],
35+
'FGFR3:c.1200_1300delinsA': {
36+
'matches': {
37+
'displayName': ['FGFR3 mutation', 'FGFR3 rearrangement'],
38+
'type': ['mutation', 'rearrangement'],
3939
}
4040
},
41-
"FGFR3:c.1200delinsACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT": {
42-
"matches": {
43-
"displayName": ["FGFR3 mutation", "FGFR3 rearrangement"],
44-
"type": ["mutation", "rearrangement"],
41+
'FGFR3:c.1200delinsACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT': {
42+
'matches': {
43+
'displayName': ['FGFR3 mutation', 'FGFR3 rearrangement'],
44+
'type': ['mutation', 'rearrangement'],
4545
}
4646
},
4747
# ambiguous structural variations -> non-structural
48-
"FGFR3:c.1200dup": {
49-
"matches": {"displayName": ["FGFR3 mutation"], "type": ["mutation"]},
50-
"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
48+
'FGFR3:c.1200dup': {
49+
'matches': {'displayName': ['FGFR3 mutation'], 'type': ['mutation']},
50+
'does_not_matches': {'displayName': ['FGFR3 rearrangement'], 'type': ['rearrangement']},
5151
},
52-
"FGFR3:c.1200_1201insA": {
53-
"matches": {"displayName": ["FGFR3 mutation"], "type": ["mutation"]},
54-
"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
52+
'FGFR3:c.1200_1201insA': {
53+
'matches': {'displayName': ['FGFR3 mutation'], 'type': ['mutation']},
54+
'does_not_matches': {'displayName': ['FGFR3 rearrangement'], 'type': ['rearrangement']},
5555
},
56-
"FGFR3:g.5000del": {
57-
"matches": {"displayName": ["FGFR3 mutation"], "type": ["mutation"]},
58-
"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
56+
'FGFR3:g.5000del': {
57+
'matches': {'displayName': ['FGFR3 mutation'], 'type': ['mutation']},
58+
'does_not_matches': {'displayName': ['FGFR3 rearrangement'], 'type': ['rearrangement']},
5959
},
60-
"FGFR3:c.1200delinsA": {
61-
"matches": {"displayName": ["FGFR3 mutation"], "type": ["mutation"]},
62-
"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
60+
'FGFR3:c.1200delinsA': {
61+
'matches': {'displayName': ['FGFR3 mutation'], 'type': ['mutation']},
62+
'does_not_matches': {'displayName': ['FGFR3 rearrangement'], 'type': ['rearrangement']},
6363
},
64-
"STK11:e.1_100del": {
65-
"matches": {"displayName": ["STK11 mutation"], "type": ["mutation"]},
66-
"does_not_matches": {"displayName": ["STK11 deletion"], "type": ["deletion"]},
64+
'STK11:e.1_100del': {
65+
'matches': {'displayName': ['STK11 mutation'], 'type': ['mutation']},
66+
'does_not_matches': {'displayName': ['STK11 deletion'], 'type': ['deletion']},
6767
},
68-
"STK11:i.1_100del": {
69-
"matches": {"displayName": ["STK11 mutation"], "type": ["mutation"]},
70-
"does_not_matches": {"displayName": ["STK11 deletion"], "type": ["deletion"]},
68+
'STK11:i.1_100del': {
69+
'matches': {'displayName': ['STK11 mutation'], 'type': ['mutation']},
70+
'does_not_matches': {'displayName': ['STK11 deletion'], 'type': ['deletion']},
7171
},
7272
# non-structural variations
73-
"FGFR3:c.1200C>A": {
74-
"matches": {"displayName": ["FGFR3 mutation"], "type": ["mutation"]},
75-
"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
73+
'FGFR3:c.1200C>A': {
74+
'matches': {'displayName': ['FGFR3 mutation'], 'type': ['mutation']},
75+
'does_not_matches': {'displayName': ['FGFR3 rearrangement'], 'type': ['rearrangement']},
7676
},
7777
}
7878

@@ -81,118 +81,118 @@
8181
# pos 1: expected equivalences
8282
ensemblProteinSample = [
8383
(
84-
"EGFR",
84+
'EGFR',
8585
[
86-
"EGFR",
87-
"ERBB",
88-
"ENSG00000146648",
89-
"ENSG00000146648.17",
90-
"ENST00000275493",
91-
"ENST00000275493.6",
92-
"NM_001346897",
93-
"NM_001346897.2",
94-
"NP_001333826",
95-
"NP_001333826.1",
86+
'EGFR',
87+
'ERBB',
88+
'ENSG00000146648',
89+
'ENSG00000146648.17',
90+
'ENST00000275493',
91+
'ENST00000275493.6',
92+
'NM_001346897',
93+
'NM_001346897.2',
94+
'NP_001333826',
95+
'NP_001333826.1',
9696
],
9797
),
9898
(
99-
"NM_001346897",
99+
'NM_001346897',
100100
[
101-
"EGFR",
102-
"ERBB",
103-
"ENSG00000146648",
104-
"ENSG00000146648.17",
105-
"NM_001346897",
106-
"NM_001346897.2",
107-
"NP_001333826",
108-
"NP_001333826.1",
101+
'EGFR',
102+
'ERBB',
103+
'ENSG00000146648',
104+
'ENSG00000146648.17',
105+
'NM_001346897',
106+
'NM_001346897.2',
107+
'NP_001333826',
108+
'NP_001333826.1',
109109
],
110110
),
111111
(
112-
"NM_001346897.2",
112+
'NM_001346897.2',
113113
[
114-
"EGFR",
115-
"ERBB",
116-
"ENSG00000146648",
117-
"ENSG00000146648.17",
118-
"NM_001346897",
119-
"NM_001346897.2",
120-
"NP_001333826",
121-
"NP_001333826.1",
114+
'EGFR',
115+
'ERBB',
116+
'ENSG00000146648',
117+
'ENSG00000146648.17',
118+
'NM_001346897',
119+
'NM_001346897.2',
120+
'NP_001333826',
121+
'NP_001333826.1',
122122
],
123123
),
124124
(
125-
"NP_001333826",
125+
'NP_001333826',
126126
[
127-
"EGFR",
128-
"ERBB",
129-
"ENSG00000146648", # Warn: Versionized ENSG won't be returned due to API limitations
130-
"NM_001346897",
131-
"NM_001346897.2",
132-
"NP_001333826",
133-
"NP_001333826.1",
127+
'EGFR',
128+
'ERBB',
129+
'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
130+
'NM_001346897',
131+
'NM_001346897.2',
132+
'NP_001333826',
133+
'NP_001333826.1',
134134
],
135135
),
136136
(
137-
"NP_001333826.1",
137+
'NP_001333826.1',
138138
[
139-
"EGFR",
140-
"ERBB",
141-
"ENSG00000146648", # Warn: Versionized ENSG won't be returned due to API limitations
142-
"NM_001346897",
143-
"NM_001346897.2",
144-
"NP_001333826",
145-
"NP_001333826.1",
139+
'EGFR',
140+
'ERBB',
141+
'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
142+
'NM_001346897',
143+
'NM_001346897.2',
144+
'NP_001333826',
145+
'NP_001333826.1',
146146
],
147147
),
148148
(
149-
"ENSG00000146648",
149+
'ENSG00000146648',
150150
[
151-
"EGFR",
152-
"ERBB",
153-
"ENSG00000146648",
154-
"ENSG00000146648.17",
155-
"ENST00000275493",
156-
"ENST00000275493.6",
157-
"NM_001346897",
158-
"NM_001346897.2",
159-
"NP_001333826", # Warn: Versionized NP won't be returned due to API limitations
151+
'EGFR',
152+
'ERBB',
153+
'ENSG00000146648',
154+
'ENSG00000146648.17',
155+
'ENST00000275493',
156+
'ENST00000275493.6',
157+
'NM_001346897',
158+
'NM_001346897.2',
159+
'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
160160
],
161161
),
162162
(
163-
"ENSG00000146648.17",
163+
'ENSG00000146648.17',
164164
[
165-
"EGFR",
166-
"ERBB",
167-
"ENSG00000146648",
168-
"ENSG00000146648.17",
169-
"ENST00000275493",
170-
"ENST00000275493.6",
171-
"NM_001346897",
172-
"NM_001346897.2",
173-
"NP_001333826", # Warn: Versionized NP won't be returned due to API limitations
165+
'EGFR',
166+
'ERBB',
167+
'ENSG00000146648',
168+
'ENSG00000146648.17',
169+
'ENST00000275493',
170+
'ENST00000275493.6',
171+
'NM_001346897',
172+
'NM_001346897.2',
173+
'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
174174
],
175175
),
176176
(
177-
"ENST00000275493",
177+
'ENST00000275493',
178178
[
179-
"EGFR",
180-
"ERBB",
181-
"ENSG00000146648",
182-
"ENSG00000146648.17",
183-
"ENST00000275493",
184-
"ENST00000275493.6",
179+
'EGFR',
180+
'ERBB',
181+
'ENSG00000146648',
182+
'ENSG00000146648.17',
183+
'ENST00000275493',
184+
'ENST00000275493.6',
185185
],
186186
),
187187
(
188-
"ENST00000275493.6",
188+
'ENST00000275493.6',
189189
[
190-
"EGFR",
191-
"ERBB",
192-
"ENSG00000146648",
193-
"ENSG00000146648.17",
194-
"ENST00000275493",
195-
"ENST00000275493.6",
190+
'EGFR',
191+
'ERBB',
192+
'ENSG00000146648',
193+
'ENSG00000146648.17',
194+
'ENST00000275493',
195+
'ENST00000275493.6',
196196
],
197197
),
198198
]

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