def _getArgCondFilter(self, rq_args, activate_it=True):
if rq_args.get("filter"):
filter_h = self.pickSolEntry("filter", rq_args["filter"])
assert filter_h is not None
else:
if "conditions" in rq_args:
cond_data = json.loads(rq_args["conditions"])
else:
cond_data = ConditionMaker.condAll()
filter_h = FilterEval(self.getEvalSpace(), cond_data)
filter_h = self.updateSolEntry("filter", filter_h)
if activate_it:
filter_h.activate()
return filter_h
def _getArgCondFilter(self, rq_args,
activate_it = True, join_cond_data = None):
filter_h, cond_data = None, None
if rq_args.get("filter"):
filter_h = self.pickSolEntry("filter", rq_args["filter"])
assert filter_h is not None, "No filter for: " + rq_args["filter"]
if join_cond_data is not None:
cond_data = filter_h.getCondDataSeq()
filter_h = None
if filter_h is None and cond_data is None:
if "conditions" in rq_args:
cond_data = json.loads(rq_args["conditions"])
else:
cond_data = ConditionMaker.condAll()
if join_cond_data is not None:
assert filter_h is None, "Filter&join collision"
cond_data = cond_data[:] + join_cond_data[:]
if filter_h is None:
filter_h = FilterEval(self.getEvalSpace(), cond_data)
filter_h = self.updateSolEntry("filter", filter_h)
if activate_it:
filter_h.activate()
return filter_h
def toJSon(self):
return ConditionMaker.joinOr([it.toJSon() for it in self.getItems()])
def toJSon(self):
return ConditionMaker.condNot(self.mBaseCond.toJSon())
def toJSon(self):
return ConditionMaker.condEnum(*self.mData)
def condition_good_confidence():
return [
ConditionMaker.condEnum("FT", ["PASS"]),
ConditionMaker.condNum("Max_GQ", min_val=50),
ConditionMaker.condNum("FS", max_val=30)
]
def condition_high_confidence():
return condition_good_confidence() + [
ConditionMaker.condNum("QUAL", min_val=40)
]
def condition_high_confidence_QD():
return condition_good_confidence() + [
ConditionMaker.condNum("QD", min_val=4)
]
def condition_consequence_xBrowse():
return ConditionMaker.condEnum("Transcript_consequence",
MODERATE_IMPACT_CSQ)
def setupSolutions_Case(app_config, base_pack):
# BGM Filters, should belong to "Undiagnosed Patients Solution Pack"
base_pack.regFilter("BGM_De_Novo", [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Callers", ["BGM_BAYES_DE_NOVO", "RUFUS"])
],
requires={"trio_base", "WS"})
base_pack.regFilter("BGM_Homozygous_Rec", [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Callers", ["BGM_HOM_REC"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Inheritance_Mode", dict(),
["Homozygous Recessive"])
],
requires={"trio_base", "WS"})
base_pack.regFilter("BGM_Compound_Het", [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Callers", ["BGM_CMPD_HET"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Compound_Het", {"approx": "transcript"},
["Proband"])
],
requires={"trio_base", "WS"})
base_pack.regFilter("BGM_Autosomal_Dominant", [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Callers", ["BGM_DE_NOVO"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"])
],
requires={"trio_base", "WS"})
# Standard mendelian Filters, should belong to
# "Undiagnosed Patients Solution Pack"
base_pack.regFilter(
"X_Linked",
condition_high_quality() + [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Inheritance_Mode", dict(), ["X-linked"])
],
requires={"trio_base", "WS"})
base_pack.regFilter(
"Mendelian_Homozygous_Rec",
condition_high_quality() + condition_all_genotypes_called() +
clinVar_not_benign() + [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Inheritance_Mode", dict(),
["Homozygous Recessive"]),
ConditionMaker.condEnum("Proband_Zygosity", ["Homozygous"])
],
requires={"trio_base", "WS"})
base_pack.regFilter(
"Mendelian_Compound_Het",
condition_high_quality() + clinVar_not_benign() + [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Compound_Het", {"approx": "transcript"},
["Proband"])
],
requires={"trio_base", "WS"})
base_pack.regFilter(
"Mendelian_Auto_Dom",
condition_high_quality() + clinVar_not_benign() + [
condition_consequence_xBrowse(),
ConditionMaker.condEnum("Transcript_biotype", ["protein_coding"]),
ConditionMaker.condEnum("Transcript_source", ["Ensembl"]),
ConditionMaker.condFunc("Inheritance_Mode", dict(),
["Autosomal Dominant"]),
ConditionMaker.condEnum("Proband_Zygosity", ["Heterozygous"])
],
requires={"trio_base", "WS"})
base_pack.regFilter(
"InSilico_Possibly_Damaging",
condition_high_confidence() + [
ConditionMaker.condEnum("Rules",
[stdNm("Possibly_Damaging_Predictions")])
],
requires={"WS"})
base_pack.regFilter(
"InSilico_Damaging",
condition_high_confidence() +
[ConditionMaker.condEnum("Rules", [stdNm("Damaging_Predictions")])],
requires={"WS"})
# SEQaBOO Filters, should belong to "Hearing Loss Solution Pack"
# base_pack.regFilter("SEQaBOO_Hearing_Loss_v_01", [
# ConditionMaker.condEnum("Rules",
# [stdNm("SEQaBOO_Hearing_Loss_v_01")]),
# ConditionMaker.condEnum("Rules", [stdNm("ACMG59")], "NOT")],
# requires = {"WS"})
# base_pack.regFilter("SEQaBOO_Hearing_Loss_v_02", [
# ConditionMaker.condEnum("Rules",
# [stdNm("SEQaBOO_Hearing_Loss_v_02")]),
# ConditionMaker.condEnum("Rules", [stdNm("ACMG59")], "NOT")],
# requires = {"WS"})
# base_pack.regFilter("SEQaBOO_Hearing_Loss_v_03", [
# ConditionMaker.condEnum("Rules",
# [stdNm("SEQaBOO_Hearing_Loss_v_03")]),
# ConditionMaker.condEnum("Rules", [stdNm("ACMG59")], "NOT")],
# requires = {"WS"})
# base_pack.regFilter("SEQaBOO_Hearing_Loss_v_03_5", [
# ConditionMaker.condEnum("Rules",
# [stdNm("SEQaBOO_Hearing_Loss_v_03")]),
# ConditionMaker.condEnum("Panels", ["All_Hearing_Loss"])],
# requires = {"WS"})
# base_pack.regFilter("SEQaBOO_Hearing_Loss_v_4", [
# ConditionMaker.condEnum("Rules", [stdNm("Hearing Loss, v.4")])],
# requires = {"WS"})
base_pack.regFilter(
"SEQaBOO_Hearing_Loss_v_5",
[ConditionMaker.condEnum("Rules", [stdNm("Hearing Loss, v.5")])],
requires={"WS"})
base_pack.regFilter(
"SEQaBOO_Hearing_Quick",
[ConditionMaker.condEnum("Rules", [stdNm("Hearing Loss Quick")])],
requires={"WS"})
# SEQaBOO Filters, should belong to "Base Solution Pack"
base_pack.regFilter("SEQaBOO_ACMG59",
[ConditionMaker.condEnum("Rules", [stdNm("ACMG59")])],
requires={"WS"})
# base_pack.regFilter("SEQaBOO_ACMG59", [
# ConditionMaker.condEnum("Rules", [stdNm("SEQaBOO_ACMG59")]),
# ConditionMaker.condEnum("Rules", [stdNm("ACMG59")], "AND")],
# requires = {"WS"})
base_pack.regFilter(
"Loss_Of_Function",
condition_high_quality() +
[ConditionMaker.condEnum("Most_Severe_Consequence", LoF_CSQ)])
base_pack.regFilter(
"Non_Synonymous",
condition_high_quality() + [
ConditionMaker.condEnum("Most_Severe_Consequence",
NON_SYNONYMOUS_CSQ)
])
base_pack.regFilter(
"UTR_and_Worse",
condition_high_quality() + [
ConditionMaker.condEnum(
"Most_Severe_Consequence", LOW_IMPACT_CSQ, join_mode="NOT")
])
base_pack.regFilter("Impact_Splicing",
condition_high_confidence() + impacting_splicing())
base_pack.regFilter(
"ClinVar_VUS_or_Worse",
condition_high_confidence() + [
ConditionMaker.condEnum("Clinvar_stars", ["1", "2", "3", "4"]),
ConditionMaker.condEnum("Clinvar_conflicts", ["True"],
join_mode="NOT"),
ConditionMaker.condEnum("Clinvar_Benign", ["VUS or Pathogenic"])
],
requires={"XL"})
base_pack.regFilter("In_Silico_Damaging",
condition_high_confidence() + [
ConditionMaker.condEnum("Polyphen_2_HVAR", ["D"]),
ConditionMaker.condEnum("SIFT", ["deleterious"])
],
requires={"XL"})
# base_pack.regFilter("Impact_Splicing",
# condition_high_quality() + impacting_splicing())
# Production Decision Trees
base_pack.regDTree("BGM Research",
cfgPathSeq(["bgm_xbrowse.pyt"]),
requires={"trio_base"})
base_pack.regDTree("BGM Red Button",
cfgPathSeq(["bgm_strict.pyt"]),
requires={"trio_base"})
base_pack.regDTree("Trio Candidates",
cfgPathSeq(["quality.pyt", "rare.pyt", "trio.pyt"]),
requires={"trio_base"})
base_pack.regDTree(
"All Rare Variants",
cfgPathSeq(["quality.pyt", "rare.pyt", "return_true.pyt"]))
# base_pack.regDTree("Hearing Loss, v.4",
# cfgPathSeq(["quality.pyt", "hearing_loss.pyt"]))
base_pack.regDTree("Hearing Loss, v.5",
cfgPathSeq(["quality.pyt", "hearing_loss_v5.pyt"]))
base_pack.regDTree("Hearing Loss Quick",
cfgPathSeq(["quality.pyt", "hearing_loss_ws.pyt"]),
requires={"WS"})
base_pack.regDTree("ACMG59 Variants",
cfgPathSeq(["quality.pyt", "acmg59.pyt"]))
base_pack.regDTree("Damaging_Predictions", cfgPathSeq(["damaging.pyt"]))
base_pack.regDTree("Possibly_Damaging_Predictions",
cfgPathSeq(["possibly_damaging.pyt"]))
# Test trees
# base_pack.regDTree("Q Test",
# cfgPathSeq(["quality.pyt", "return_true.pyt"]))
# base_pack.regDTree("R Test",
# cfgPathSeq(["rare.pyt", "return_true.pyt"]))
# base_pack.regDTree("T Test",
# [cfgPath("trio.pyt")],
# requires = {"trio_base"})
# base_pack.regDTree("H Test",
# [cfgPath("hearing_loss.pyt")])
base_pack.regZone("Gene", "Symbol")
base_pack.regZone("Gene List", "Panels")
base_pack.regZone("Sample", "Has_Variant")
base_pack.regZone("Cohort", "Variant_in", requires={"cohorts"})
base_pack.regZone("Tag", "_tags")
demo_tab_schema = ReportTabSchema("demo", use_tags=True)
demo_tab_schema.addField("gene(s)", "/_view/general/genes[]")
demo_tab_schema.addField("variant", "/__data/label")
demo_tab_schema.addField("gnomAD_AF", "/_filters/gnomad_af_fam")
base_pack.regTabSchema(demo_tab_schema)
def clinVar_not_benign():
return [
ConditionMaker.condEnum("Clinvar_Trusted_Simplified", ["benign"],
"NOT")
]
def impacting_splicing():
return [ConditionMaker.condNum("splice_ai_dsmax", min_val=0.2)]
def condition_all_genotypes_called():
return [ConditionMaker.condNum("Num_NO_CALL", max_val=0)]
def condition_high_quality_all_samples():
return [ConditionMaker.condNum("Min_GQ", min_val=40)]
