Merge pull request #102 from bcgsc/release/v1.12.0

Release/v1.12.0

Author: mathieulemieux

graphkb/constants.py

@@ -11,102 +11,102 @@
 
 PREFERRED_GENE_SOURCE = "#39:5"  # HGNC
 
-BASE_RETURN_PROPERTIES = ['@rid', '@class']
+BASE_RETURN_PROPERTIES = ["@rid", "@class"]
 
 GENERIC_RETURN_PROPERTIES = [
-    'name',
-    'sourceId',
-    'sourceIdVersion',
-    'source.name',
-    'source.@rid',
-    'displayName',
-    'deprecated',
+    "name",
+    "sourceId",
+    "sourceIdVersion",
+    "source.name",
+    "source.@rid",
+    "displayName",
+    "deprecated",
 ] + BASE_RETURN_PROPERTIES
 
-GENE_RETURN_PROPERTIES = ['biotype'] + GENERIC_RETURN_PROPERTIES
+GENE_RETURN_PROPERTIES = ["biotype"] + GENERIC_RETURN_PROPERTIES
 
 VARIANT_RETURN_PROPERTIES = (
     BASE_RETURN_PROPERTIES
-    + [f'type.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + [f'reference1.{p}' for p in GENE_RETURN_PROPERTIES]
-    + [f'reference2.{p}' for p in GENE_RETURN_PROPERTIES]
-    + ['zygosity', 'germline', 'displayName']
+    + [f"type.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + [f"reference1.{p}" for p in GENE_RETURN_PROPERTIES]
+    + [f"reference2.{p}" for p in GENE_RETURN_PROPERTIES]
+    + ["zygosity", "germline", "displayName"]
 )
 
 POS_VARIANT_RETURN_PROPERTIES = VARIANT_RETURN_PROPERTIES + [
-    'break1Start',
-    'break1End',
-    'break2Start',
-    'break2End',
-    'break1Repr',
-    'break2Repr',
-    'refSeq',
-    'untemplatedSeq',
-    'untemplatedSeqSize',
-    'truncation',
-    'assembly',
+    "break1Start",
+    "break1End",
+    "break2Start",
+    "break2End",
+    "break1Repr",
+    "break2Repr",
+    "refSeq",
+    "untemplatedSeq",
+    "untemplatedSeqSize",
+    "truncation",
+    "assembly",
 ]
 
 STATEMENT_RETURN_PROPERTIES = (
     BASE_RETURN_PROPERTIES
-    + ['displayNameTemplate', 'sourceId', 'source.name', 'source.displayName']
-    + [f'conditions.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + [f'subject.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + [f'evidence.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + [f'relevance.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + [f'evidenceLevel.{p}' for p in GENERIC_RETURN_PROPERTIES]
-    + ['reviewStatus']
+    + ["displayNameTemplate", "sourceId", "source.name", "source.displayName"]
+    + [f"conditions.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + [f"subject.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + [f"evidence.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + [f"relevance.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + [f"evidenceLevel.{p}" for p in GENERIC_RETURN_PROPERTIES]
+    + ["reviewStatus"]
 )
 
 
-ONCOKB_SOURCE_NAME = 'oncokb'
-ONCOGENE = 'oncogenic'
-TUMOUR_SUPPRESSIVE = 'tumour suppressive'
-FUSION_NAMES = ['structural variant', 'fusion']
+ONCOKB_SOURCE_NAME = "oncokb"
+ONCOGENE = "oncogenic"
+TUMOUR_SUPPRESSIVE = "tumour suppressive"
+FUSION_NAMES = ["structural variant", "fusion"]
 
 PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]
 
-BASE_THERAPEUTIC_TERMS = ['therapeutic efficacy', 'eligibility']
+BASE_THERAPEUTIC_TERMS = ["therapeutic efficacy", "eligibility"]
 # the order here is the order these are applied, the first category matched is returned
 RELEVANCE_BASE_TERMS: CategoryBaseTermMapping = [
-    ('therapeutic', BASE_THERAPEUTIC_TERMS),
-    ('diagnostic', ['diagnostic indicator']),
-    ('prognostic', ['prognostic indicator']),
-    ('pharmacogenomic', ['metabolism', 'toxicity', 'dosage']),
-    ('cancer predisposition', ['pathogenic']),
-    ('biological', ['functional effect', 'tumourigenesis', 'predisposing']),
+    ("therapeutic", BASE_THERAPEUTIC_TERMS),
+    ("diagnostic", ["diagnostic indicator"]),
+    ("prognostic", ["prognostic indicator"]),
+    ("pharmacogenomic", ["metabolism", "toxicity", "dosage"]),
+    ("cancer predisposition", ["pathogenic"]),
+    ("biological", ["functional effect", "tumourigenesis", "predisposing"]),
 ]
-FAILED_REVIEW_STATUS = 'failed'
+FAILED_REVIEW_STATUS = "failed"
 
-CHROMOSOMES_HG38 = [f"chr{i}" for i in range(1, 23)] + ['chrX', 'chrY', 'chrM']
-CHROMOSOMES_HG19 = [str(i) for i in range(1, 23)] + ['x', 'y', 'mt']
+CHROMOSOMES_HG38 = [f"chr{i}" for i in range(1, 23)] + ["chrX", "chrY", "chrM"]
+CHROMOSOMES_HG19 = [str(i) for i in range(1, 23)] + ["x", "y", "mt"]
 CHROMOSOMES = CHROMOSOMES_HG38 + CHROMOSOMES_HG19
 
-AMBIGUOUS_AA = ['x', '?', 'X']
+AMBIGUOUS_AA = ["x", "?", "X"]
 AA_3to1_MAPPING = {
-    'Ala': 'A',
-    'Arg': 'R',
-    'Asn': 'N',
-    'Asp': 'D',
-    'Asx': 'B',
-    'Cys': 'C',
-    'Glu': 'E',
-    'Gln': 'Q',
-    'Glx': 'Z',
-    'Gly': 'G',
-    'His': 'H',
-    'Ile': 'I',
-    'Leu': 'L',
-    'Lys': 'K',
-    'Met': 'M',
-    'Phe': 'F',
-    'Pro': 'P',
-    'Ser': 'S',
-    'Thr': 'T',
-    'Trp': 'W',
-    'Tyr': 'Y',
-    'Val': 'V',
-    'Ter': '*',
+    "Ala": "A",
+    "Arg": "R",
+    "Asn": "N",
+    "Asp": "D",
+    "Asx": "B",
+    "Cys": "C",
+    "Glu": "E",
+    "Gln": "Q",
+    "Glx": "Z",
+    "Gly": "G",
+    "His": "H",
+    "Ile": "I",
+    "Leu": "L",
+    "Lys": "K",
+    "Met": "M",
+    "Phe": "F",
+    "Pro": "P",
+    "Ser": "S",
+    "Thr": "T",
+    "Trp": "W",
+    "Tyr": "Y",
+    "Val": "V",
+    "Ter": "*",
 }
 
 
@@ -128,47 +128,89 @@ def __getitem__(self, key):
 
 
 INPUT_COPY_CATEGORIES = IterableNamespace(
-    AMP='amplification',
-    ANY_GAIN='copy gain',
-    ANY_LOSS='copy loss',
-    DEEP='deep deletion',
-    GAIN='low level copy gain',
-    LOSS='shallow deletion',
+    AMP="amplification",
+    ANY_GAIN="copy gain",
+    ANY_LOSS="copy loss",
+    DEEP="deep deletion",
+    GAIN="low level copy gain",
+    LOSS="shallow deletion",
 )
 INPUT_EXPRESSION_CATEGORIES = IterableNamespace(
-    UP='increased expression', DOWN='reduced expression'
+    UP="increased expression", DOWN="reduced expression"
 )
 
 # From: https://github.com/bcgsc/pori_graphkb_parser/blob/ae3738842a4c208ab30f58c08ae987594d632504/src/constants.ts#L33-L80
 TYPES_TO_NOTATION: Dict[str, str] = {
-    'acetylation': 'ac',
-    'copy gain': 'copygain',
-    'copy loss': 'copyloss',
-    'deletion': 'del',
-    'duplication': 'dup',
-    'extension': 'ext',
-    'frameshift': 'fs',
-    'fusion': 'fusion',
-    'indel': 'delins',
-    'insertion': 'ins',
-    'inversion': 'inv',
-    'inverted translocation': 'itrans',
-    'methylation': 'me',
-    'missense mutation': 'mis',
-    'mutation': 'mut',
-    'nonsense mutation': '>',
-    'phosphorylation': 'phos',
-    'splice-site': 'spl',
-    'substitution': '>',
-    'translocation': 'trans',
-    'truncating frameshift mutation': 'fs',
-    'ubiquitination': 'ub',
+    "acetylation": "ac",
+    "copy gain": "copygain",
+    "copy loss": "copyloss",
+    "deletion": "del",
+    "duplication": "dup",
+    "extension": "ext",
+    "frameshift": "fs",
+    "fusion": "fusion",
+    "indel": "delins",
+    "insertion": "ins",
+    "inversion": "inv",
+    "inverted translocation": "itrans",
+    "methylation": "me",
+    "missense mutation": "mis",
+    "mutation": "mut",
+    "nonsense mutation": ">",
+    "phosphorylation": "phos",
+    "splice-site": "spl",
+    "substitution": ">",
+    "translocation": "trans",
+    "truncating frameshift mutation": "fs",
+    "ubiquitination": "ub",
     # deprecated forms and aliases
-    'frameshift mutation': 'fs',
-    'frameshift truncation': 'fs',
-    'missense variant': 'mis',
-    'truncating frameshift': 'fs',
-    'missense': 'mis',
-    'mutations': 'mut',
-    'nonsense': '>',
+    "frameshift mutation": "fs",
+    "frameshift truncation": "fs",
+    "missense variant": "mis",
+    "truncating frameshift": "fs",
+    "missense": "mis",
+    "mutations": "mut",
+    "nonsense": ">",
 }
+
+# For match.type_screening() [KBDEV-1056]
+DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = 'mutation'
+STRUCTURAL_VARIANT_SIZE_THRESHOLD = 48  # bp
+STRUCTURAL_VARIANT_TYPES = [
+    "structural variant",
+    "insertion",
+    "in-frame insertion",
+    "deletion",
+    "deletion polymorphism",
+    "in-frame deletion",
+    "translocation",
+    "inverted translocation",
+    "inversion",
+    "indel",
+    "fusion",
+    "out-of-frame fusion",
+    "oncogenic fusion",
+    "in-frame fusion",
+    "disruptive fusion",
+    "duplication",
+    "internal duplication",
+    "tandem duplication",
+    "internal tandem duplication",
+    "itd",
+    "domain duplication",
+    "kinase domain duplication",
+    "copy variant",
+    "copy number variation",
+    "copy number variant",
+    "copy loss",
+    "copy number loss",
+    "shallow deletion",
+    "deep deletion",
+    "gene deletion",
+    "copy gain",
+    "copy number gain",
+    "low level copy gain",
+    "amplification",
+    "focal amplification",
+    "rearrangement",
+]