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‎pori_python/graphkb/constants.py‎

Lines changed: 147 additions & 147 deletions
Original file line numberDiff line numberDiff line change
@@ -5,107 +5,107 @@
55

66
DEFAULT_LIMIT = 1000
77

8-
PREFERRED_GENE_SOURCE_NAME = "HGNC"
8+
PREFERRED_GENE_SOURCE_NAME = 'HGNC'
99

10-
BASE_RETURN_PROPERTIES = ["@rid", "@class"]
10+
BASE_RETURN_PROPERTIES = ['@rid', '@class']
1111

1212
GENERIC_RETURN_PROPERTIES = [
13-
"name",
14-
"sourceId",
15-
"sourceIdVersion",
16-
"source.name",
17-
"source.@rid",
18-
"displayName",
19-
"deprecated",
13+
'name',
14+
'sourceId',
15+
'sourceIdVersion',
16+
'source.name',
17+
'source.@rid',
18+
'displayName',
19+
'deprecated',
2020
] + BASE_RETURN_PROPERTIES
2121

22-
GENE_RETURN_PROPERTIES = ["biotype"] + GENERIC_RETURN_PROPERTIES
22+
GENE_RETURN_PROPERTIES = ['biotype'] + GENERIC_RETURN_PROPERTIES
2323

2424
VARIANT_RETURN_PROPERTIES = (
2525
BASE_RETURN_PROPERTIES
26-
+ [f"type.{p}" for p in GENERIC_RETURN_PROPERTIES]
27-
+ [f"reference1.{p}" for p in GENE_RETURN_PROPERTIES]
28-
+ [f"reference2.{p}" for p in GENE_RETURN_PROPERTIES]
29-
+ ["zygosity", "germline", "displayName"]
26+
+ [f'type.{p}' for p in GENERIC_RETURN_PROPERTIES]
27+
+ [f'reference1.{p}' for p in GENE_RETURN_PROPERTIES]
28+
+ [f'reference2.{p}' for p in GENE_RETURN_PROPERTIES]
29+
+ ['zygosity', 'germline', 'displayName']
3030
)
3131

3232
POS_VARIANT_RETURN_PROPERTIES = VARIANT_RETURN_PROPERTIES + [
33-
"break1Start",
34-
"break1End",
35-
"break2Start",
36-
"break2End",
37-
"break1Repr",
38-
"break2Repr",
39-
"refSeq",
40-
"untemplatedSeq",
41-
"untemplatedSeqSize",
42-
"truncation",
43-
"assembly",
33+
'break1Start',
34+
'break1End',
35+
'break2Start',
36+
'break2End',
37+
'break1Repr',
38+
'break2Repr',
39+
'refSeq',
40+
'untemplatedSeq',
41+
'untemplatedSeqSize',
42+
'truncation',
43+
'assembly',
4444
]
4545

4646
STATEMENT_RETURN_PROPERTIES = (
4747
BASE_RETURN_PROPERTIES
48-
+ ["displayNameTemplate", "sourceId", "source.name", "source.displayName"]
49-
+ [f"conditions.{p}" for p in GENERIC_RETURN_PROPERTIES]
50-
+ [f"subject.{p}" for p in GENERIC_RETURN_PROPERTIES]
51-
+ [f"evidence.{p}" for p in GENERIC_RETURN_PROPERTIES]
52-
+ [f"relevance.{p}" for p in GENERIC_RETURN_PROPERTIES]
53-
+ [f"evidenceLevel.{p}" for p in GENERIC_RETURN_PROPERTIES]
54-
+ ["reviewStatus"]
48+
+ ['displayNameTemplate', 'sourceId', 'source.name', 'source.displayName']
49+
+ [f'conditions.{p}' for p in GENERIC_RETURN_PROPERTIES]
50+
+ [f'subject.{p}' for p in GENERIC_RETURN_PROPERTIES]
51+
+ [f'evidence.{p}' for p in GENERIC_RETURN_PROPERTIES]
52+
+ [f'relevance.{p}' for p in GENERIC_RETURN_PROPERTIES]
53+
+ [f'evidenceLevel.{p}' for p in GENERIC_RETURN_PROPERTIES]
54+
+ ['reviewStatus']
5555
)
5656

5757

58-
ONCOKB_SOURCE_NAME = "oncokb"
59-
TSO500_SOURCE_NAME = "tso500"
60-
ONCOGENE = "oncogenic"
61-
TUMOUR_SUPPRESSIVE = "tumour suppressive"
62-
CANCER_GENE = "cancer gene"
63-
FUSION_NAMES = ["structural variant", "fusion"]
58+
ONCOKB_SOURCE_NAME = 'oncokb'
59+
TSO500_SOURCE_NAME = 'tso500'
60+
ONCOGENE = 'oncogenic'
61+
TUMOUR_SUPPRESSIVE = 'tumour suppressive'
62+
CANCER_GENE = 'cancer gene'
63+
FUSION_NAMES = ['structural variant', 'fusion']
6464

65-
GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]
66-
GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST = ["CGI", "CIViC"]
65+
GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ['cancer genome interpreter', 'civic']
66+
GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST = ['CGI', 'CIViC']
6767

68-
BASE_THERAPEUTIC_TERMS = ["therapeutic efficacy", "eligibility"]
68+
BASE_THERAPEUTIC_TERMS = ['therapeutic efficacy', 'eligibility']
6969
# the order here is the order these are applied, the first category matched is returned
7070
RELEVANCE_BASE_TERMS: CategoryBaseTermMapping = [
71-
("therapeutic", BASE_THERAPEUTIC_TERMS),
72-
("diagnostic", ["diagnostic indicator"]),
73-
("prognostic", ["prognostic indicator"]),
74-
("pharmacogenomic", ["metabolism", "toxicity", "dosage"]),
75-
("cancer predisposition", ["pathogenic"]),
76-
("biological", ["functional effect", "tumourigenesis", "predisposing"]),
71+
('therapeutic', BASE_THERAPEUTIC_TERMS),
72+
('diagnostic', ['diagnostic indicator']),
73+
('prognostic', ['prognostic indicator']),
74+
('pharmacogenomic', ['metabolism', 'toxicity', 'dosage']),
75+
('cancer predisposition', ['pathogenic']),
76+
('biological', ['functional effect', 'tumourigenesis', 'predisposing']),
7777
]
78-
FAILED_REVIEW_STATUS = "failed"
78+
FAILED_REVIEW_STATUS = 'failed'
7979

80-
CHROMOSOMES_HG38 = [f"chr{i}" for i in range(1, 23)] + ["chrX", "chrY", "chrM"]
81-
CHROMOSOMES_HG19 = [str(i) for i in range(1, 23)] + ["x", "y", "mt"]
80+
CHROMOSOMES_HG38 = [f'chr{i}' for i in range(1, 23)] + ['chrX', 'chrY', 'chrM']
81+
CHROMOSOMES_HG19 = [str(i) for i in range(1, 23)] + ['x', 'y', 'mt']
8282
CHROMOSOMES = CHROMOSOMES_HG38 + CHROMOSOMES_HG19
8383

84-
AMBIGUOUS_AA = ["x", "?", "X"]
84+
AMBIGUOUS_AA = ['x', '?', 'X']
8585
AA_3to1_MAPPING = {
86-
"Ala": "A",
87-
"Arg": "R",
88-
"Asn": "N",
89-
"Asp": "D",
90-
"Asx": "B",
91-
"Cys": "C",
92-
"Glu": "E",
93-
"Gln": "Q",
94-
"Glx": "Z",
95-
"Gly": "G",
96-
"His": "H",
97-
"Ile": "I",
98-
"Leu": "L",
99-
"Lys": "K",
100-
"Met": "M",
101-
"Phe": "F",
102-
"Pro": "P",
103-
"Ser": "S",
104-
"Thr": "T",
105-
"Trp": "W",
106-
"Tyr": "Y",
107-
"Val": "V",
108-
"Ter": "*",
86+
'Ala': 'A',
87+
'Arg': 'R',
88+
'Asn': 'N',
89+
'Asp': 'D',
90+
'Asx': 'B',
91+
'Cys': 'C',
92+
'Glu': 'E',
93+
'Gln': 'Q',
94+
'Glx': 'Z',
95+
'Gly': 'G',
96+
'His': 'H',
97+
'Ile': 'I',
98+
'Leu': 'L',
99+
'Lys': 'K',
100+
'Met': 'M',
101+
'Phe': 'F',
102+
'Pro': 'P',
103+
'Ser': 'S',
104+
'Thr': 'T',
105+
'Trp': 'W',
106+
'Tyr': 'Y',
107+
'Val': 'V',
108+
'Ter': '*',
109109
}
110110

111111

@@ -127,89 +127,89 @@ def __getitem__(self, key):
127127

128128

129129
INPUT_COPY_CATEGORIES = IterableNamespace(
130-
AMP="amplification",
131-
ANY_GAIN="copy gain",
132-
ANY_LOSS="copy loss",
133-
DEEP="deep deletion",
134-
GAIN="low level copy gain",
135-
LOSS="shallow deletion",
130+
AMP='amplification',
131+
ANY_GAIN='copy gain',
132+
ANY_LOSS='copy loss',
133+
DEEP='deep deletion',
134+
GAIN='low level copy gain',
135+
LOSS='shallow deletion',
136136
)
137137
INPUT_EXPRESSION_CATEGORIES = IterableNamespace(
138-
UP="increased expression", DOWN="reduced expression"
138+
UP='increased expression', DOWN='reduced expression'
139139
)
140140

141141
# From: https://github.com/bcgsc/pori_graphkb_parser/blob/ae3738842a4c208ab30f58c08ae987594d632504/src/constants.ts#L33-L80
142142
TYPES_TO_NOTATION: Dict[str, str] = {
143-
"acetylation": "ac",
144-
"copy gain": "copygain",
145-
"copy loss": "copyloss",
146-
"deletion": "del",
147-
"duplication": "dup",
148-
"extension": "ext",
149-
"frameshift": "fs",
150-
"fusion": "fusion",
151-
"indel": "delins",
152-
"insertion": "ins",
153-
"inversion": "inv",
154-
"inverted translocation": "itrans",
155-
"methylation": "me",
156-
"missense mutation": "mis",
157-
"mutation": "mut",
158-
"nonsense mutation": ">",
159-
"phosphorylation": "phos",
160-
"splice-site": "spl",
161-
"substitution": ">",
162-
"translocation": "trans",
163-
"truncating frameshift mutation": "fs",
164-
"ubiquitination": "ub",
143+
'acetylation': 'ac',
144+
'copy gain': 'copygain',
145+
'copy loss': 'copyloss',
146+
'deletion': 'del',
147+
'duplication': 'dup',
148+
'extension': 'ext',
149+
'frameshift': 'fs',
150+
'fusion': 'fusion',
151+
'indel': 'delins',
152+
'insertion': 'ins',
153+
'inversion': 'inv',
154+
'inverted translocation': 'itrans',
155+
'methylation': 'me',
156+
'missense mutation': 'mis',
157+
'mutation': 'mut',
158+
'nonsense mutation': '>',
159+
'phosphorylation': 'phos',
160+
'splice-site': 'spl',
161+
'substitution': '>',
162+
'translocation': 'trans',
163+
'truncating frameshift mutation': 'fs',
164+
'ubiquitination': 'ub',
165165
# deprecated forms and aliases
166-
"frameshift mutation": "fs",
167-
"frameshift truncation": "fs",
168-
"missense variant": "mis",
169-
"truncating frameshift": "fs",
170-
"missense": "mis",
171-
"mutations": "mut",
172-
"nonsense": ">",
166+
'frameshift mutation': 'fs',
167+
'frameshift truncation': 'fs',
168+
'missense variant': 'mis',
169+
'truncating frameshift': 'fs',
170+
'missense': 'mis',
171+
'mutations': 'mut',
172+
'nonsense': '>',
173173
}
174174

175175
# For match.type_screening() [KBDEV-1056]
176-
DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = "mutation"
176+
DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = 'mutation'
177177
STRUCTURAL_VARIANT_SIZE_THRESHOLD = 48 # bp
178178
STRUCTURAL_VARIANT_TYPES = [
179-
"structural variant",
180-
"insertion",
181-
"in-frame insertion",
182-
"deletion",
183-
"deletion polymorphism",
184-
"in-frame deletion",
185-
"translocation",
186-
"inverted translocation",
187-
"inversion",
188-
"indel",
189-
"fusion",
190-
"out-of-frame fusion",
191-
"oncogenic fusion",
192-
"in-frame fusion",
193-
"disruptive fusion",
194-
"duplication",
195-
"internal duplication",
196-
"tandem duplication",
197-
"internal tandem duplication",
198-
"itd",
199-
"domain duplication",
200-
"kinase domain duplication",
201-
"copy variant",
202-
"copy number variation",
203-
"copy number variant",
204-
"copy loss",
205-
"copy number loss",
206-
"shallow deletion",
207-
"deep deletion",
208-
"gene deletion",
209-
"copy gain",
210-
"copy number gain",
211-
"low level copy gain",
212-
"amplification",
213-
"focal amplification",
214-
"rearrangement",
179+
'structural variant',
180+
'insertion',
181+
'in-frame insertion',
182+
'deletion',
183+
'deletion polymorphism',
184+
'in-frame deletion',
185+
'translocation',
186+
'inverted translocation',
187+
'inversion',
188+
'indel',
189+
'fusion',
190+
'out-of-frame fusion',
191+
'oncogenic fusion',
192+
'in-frame fusion',
193+
'disruptive fusion',
194+
'duplication',
195+
'internal duplication',
196+
'tandem duplication',
197+
'internal tandem duplication',
198+
'itd',
199+
'domain duplication',
200+
'kinase domain duplication',
201+
'copy variant',
202+
'copy number variation',
203+
'copy number variant',
204+
'copy loss',
205+
'copy number loss',
206+
'shallow deletion',
207+
'deep deletion',
208+
'gene deletion',
209+
'copy gain',
210+
'copy number gain',
211+
'low level copy gain',
212+
'amplification',
213+
'focal amplification',
214+
'rearrangement',
215215
]

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