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Feature/pcgr v2.2.1 (#10)
1 parent 8780e2f commit f84fbcd

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9 files changed

+145
-140
lines changed

9 files changed

+145
-140
lines changed

‎bolt/common/constants.py‎

Lines changed: 32 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -35,9 +35,9 @@
3535
'pathogenic',
3636
'uncertain_significance',
3737
}
38-
PCGR_TIERS_RESCUE = {
39-
'TIER_1',
40-
'TIER_2',
38+
PCGR_ACTIONABILITY_TIER_RESCUE = {
39+
'1',
40+
'2',
4141
}
4242

4343

@@ -116,16 +116,14 @@ class VcfInfo(enum.Enum):
116116
SAGE_NOVEL = 'SAGE_NOVEL'
117117
SAGE_RESCUE = 'SAGE_RESCUE'
118118

119-
PCGR_TIER = 'PCGR_TIER'
119+
PCGR_ACTIONABILITY_TIER = 'PCGR_ACTIONABILITY_TIER'
120120
PCGR_CSQ = 'PCGR_CSQ'
121121
PCGR_MUTATION_HOTSPOT = 'PCGR_MUTATION_HOTSPOT'
122-
PCGR_CLINVAR_CLNSIG = 'PCGR_CLINVAR_CLNSIG'
122+
PCGR_CLINVAR_CLASSIFICATION = 'PCGR_CLINVAR_CLASSIFICATION'
123123
PCGR_COSMIC_COUNT = 'PCGR_COSMIC_COUNT'
124124
PCGR_TCGA_PANCANCER_COUNT = 'PCGR_TCGA_PANCANCER_COUNT'
125125
PCGR_ICGC_PCAWG_COUNT = 'PCGR_ICGC_PCAWG_COUNT'
126126

127-
CPSR_FINAL_CLASSIFICATION = 'CPSR_FINAL_CLASSIFICATION'
128-
CPSR_PATHOGENICITY_SCORE = 'CPSR_PATHOGENICITY_SCORE'
129127
CPSR_CLINVAR_CLASSIFICATION = 'CPSR_CLINVAR_CLASSIFICATION'
130128
CPSR_CSQ = 'CPSR_CSQ'
131129

@@ -151,7 +149,7 @@ class VcfInfo(enum.Enum):
151149

152150
GNOMAD_AF = 'gnomAD_AF'
153151

154-
PCGR_TIER_RESCUE = 'PCGR_TIER_RESCUE'
152+
PCGR_ACTIONABILITY_TIER_RESCUE = 'PCGR_ACTIONABILITY_TIER_RESCUE'
155153
SAGE_HOTSPOT_RESCUE = 'SAGE_HOTSPOT_RESCUE'
156154
CLINICAL_POTENTIAL_RESCUE = 'CLINICAL_POTENTIAL_RESCUE'
157155

@@ -270,7 +268,7 @@ def namespace(self):
270268
'Description': 'Variant rescued by a matching SAGE call',
271269
},
272270

273-
VcfInfo.PCGR_TIER: {
271+
VcfInfo.PCGR_ACTIONABILITY_TIER: {
274272
'Number': '1',
275273
'Type': 'String',
276274
'Description': (
@@ -281,28 +279,29 @@ def namespace(self):
281279
},
282280
VcfInfo.PCGR_CSQ: {
283281
'Number': '.',
284-
'Type': 'String',
285-
'Description': (
286-
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|'
287-
'Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|'
288-
'CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|'
289-
'DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|'
290-
'MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|'
291-
'UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|'
292-
'gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|'
293-
'gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|'
294-
'NearestExonJB'
295-
),
282+
'Type': 'String',
283+
'Description': (
284+
'Consequence annotations from Ensembl VEP. Format: '
285+
'Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|'
286+
'HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|'
287+
'ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|'
288+
'MANE|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|'
289+
'UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|'
290+
'gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|'
291+
'gnomADe_REMAINING_AF|gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|'
292+
'MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|'
293+
'MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref'
294+
),
296295
},
297296
VcfInfo.PCGR_MUTATION_HOTSPOT: {
298297
'Number': '.',
299298
'Type': 'String',
300-
'Description': 'Known cancer mutation hotspot, as found in cancerhotspots.org_v2, Gene|Codon|Q-value',
299+
'Description': 'Known cancer mutation hotspot, as found in cancerhotspots.org. Format: GeneSymbol|Entrez_ID|CodonRefAA|Alt_AA|Q-value',
301300
},
302-
VcfInfo.PCGR_CLINVAR_CLNSIG: {
301+
VcfInfo.PCGR_CLINVAR_CLASSIFICATION: {
303302
'Number': '.',
304303
'Type': 'String',
305-
'Description': 'ClinVar clinical significance',
304+
'Description': 'ClinVar - clinical significance - per phenotype submission',
306305
},
307306
VcfInfo.PCGR_COSMIC_COUNT: {
308307
'Number': '1',
@@ -320,23 +319,10 @@ def namespace(self):
320319
'Description': 'Count of ICGC PCAWG hits',
321320
},
322321

323-
VcfInfo.CPSR_FINAL_CLASSIFICATION: {
324-
'Number': '1',
325-
'Type': 'String',
326-
'Description': (
327-
'Final variant classification based on the combination of CLINVAR_CLASSIFICTION (for '
328-
'ClinVar-classified variants), and CPSR_CLASSIFICATION (for novel variants)'
329-
),
330-
},
331-
VcfInfo.CPSR_PATHOGENICITY_SCORE: {
332-
'Number': '1',
333-
'Type': 'Float',
334-
'Description': 'Aggregated CPSR pathogenicity score',
335-
},
336322
VcfInfo.CPSR_CLINVAR_CLASSIFICATION: {
337323
'Number': '1',
338324
'Type': 'String',
339-
'Description': 'Clinical significance of variant on a five-tiered scale',
325+
'Description': 'ClinVar - Overall clinical significance of variant on a five-tiered scale',
340326
},
341327
VcfInfo.CPSR_CSQ: {
342328
'Number': '.',
@@ -345,13 +331,13 @@ def namespace(self):
345331
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|'
346332
'Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|'
347333
'Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|'
348-
'FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE_SELECT|'
349-
'MANE_PLUS_CLINICAL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|'
350-
'DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF|gnomAD_AFR_AF|'
351-
'gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|'
352-
'gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|'
353-
'MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|LoF|LoF_filter|LoF_flags|'
354-
'LoF_info'
334+
'FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|MANE_SELECT|'
335+
'MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|'
336+
'DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|'
337+
'gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|gnomADe_REMAINING_AF|'
338+
'gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|'
339+
'MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|MaxEntScan_alt|MaxEntScan_diff|'
340+
'MaxEntScan_ref'
355341
),
356342
},
357343

@@ -360,7 +346,7 @@ def namespace(self):
360346
'Type': 'Flag',
361347
'Description': '',
362348
},
363-
VcfInfo.PCGR_TIER_RESCUE: {
349+
VcfInfo.PCGR_ACTIONABILITY_TIER_RESCUE: {
364350
'Number': '0',
365351
'Type': 'Flag',
366352
'Description': '',

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