Documentation
¶
Index ¶
- Variables
- func AddClnsigConf(item map[string]string) string
- func AddTier(item map[string]string, stats map[string]int, ...)
- func CHgvsAlt(cHgvs string) string
- func CheckAF(item map[string]string, AFlist []string, threshold float64) bool
- func CnvPrimer(item map[string]string, cnvType string) (primer string)
- func ExonPrimer(item map[string]string) (primer string, primerMap map[string]string)
- func FamilyTag(item map[string]string, inheritDb map[string]map[string]int, tag string) string
- func FloatFormat(item map[string]string)
- func Format(item map[string]string)
- func GetFromMultiKeys(db map[string]map[string]string, keys []string) (info map[string]string, hit bool)
- func GetKeys(transcript, cHGVS string) (keys []string)
- func GetPath(key, dbPath string, config map[string]interface{}) (path string)
- func GetStrVal(key string, config map[string]interface{}) (val string)
- func GuessPath(path, dbPath string) string
- func InheritCheck(item map[string]string, inheritDb map[string]map[string]int)
- func InheritCoincide(item map[string]string, inheritDb map[string]map[string]int, isTrio bool) string
- func InheritFrom(item map[string]string, sampleList []string) string
- func InheritFrom2(item map[string]string, sampleList []string) string
- func LargePrimer(item map[string]string) (primer string)
- func LoadGeneTrans(fileName string)
- func NewlineFormat(item map[string]string)
- func ParseSpliceAI(item map[string]string)
- func PrimerDesign(item map[string]string) string
- func Score2Pred(item map[string]string)
- func UpdateAutoRule(item map[string]string)
- func UpdateCnvAnnot(geneLst, key string, item, gene2id map[string]string, ...)
- func UpdateDisGenes(sep string, genes []string, item, gene2id, geneDisDbCol map[string]string, ...)
- func UpdateDisease(geneID string, item, gDiseaseDbColumn map[string]string, ...)
- func UpdateFuncRegion(item map[string]string)
- func UpdateFunction(item map[string]string)
- func UpdateGeneDb(geneList string, item, geneDb map[string]string)
- func UpdateManualRule(item map[string]string)
- func UpdateRedis(item map[string]string, db *redis.Client, keyPrefix string)
- func UpdateSnv(item map[string]string, gender string)
- func UpdateSnvTier1(item map[string]string)
- func UpdateTags(item map[string]string, specVarDb map[string]bool, isTrio, isTrio2 bool) string
- func UpdateZygosity(item map[string]string, gender string)
- func ZygosityFormat(zygosity string) string
- type AnnoDb
- type EncodeDb
Constants ¶
This section is empty.
Variables ¶
View Source
var ( Tier1AFThreshold = 0.01 Tier1PLPAFThreshold = 0.05 // in-house WGS AF threshold Tier1InHouseAFThreshold = 0.01 )
View Source
var AFlist = []string{
"GnomAD EAS AF",
"GnomAD AF",
"1000G AF",
"ESP6500 AF",
"ExAC EAS AF",
"ExAC AF",
"PVFD AF",
"Panel AlleleFreq",
"wgs_GnomAD_AF",
}
AFlist default AF list for check
View Source
var FuncInfo = map[string]int{
"splice-3": 3,
"splice_acceptor_variant": 3,
"splice-5": 3,
"splice_donor_variant": 3,
"init-loss": 3,
"start_lost": 3,
"alt-start": 3,
"start_retained_variant": 3,
"frameshift": 3,
"frameshift_variant": 3,
"nonsense": 3,
"stop-gain": 3,
"stop_gained": 3,
"span": 3,
"stop-loss": 2,
"stop_lost": 2,
"missense": 2,
"missense_variant": 2,
"cds-del": 2,
"inframe_deletion": 2,
"cds-indel": 2,
"cds-ins": 2,
"inframe_insertion": 2,
"splice-10": 2,
"splice+10": 2,
"coding-synon": 1,
"synonymous_variant": 1,
"splice-20": 1,
"splice+20": 1,
}
FuncInfo classify function Tier1 >1 LoF 3 VEP: cds-indel span splice+-10 splice+-20
View Source
var HomFixRatioThreshold = 0.85
View Source
var (
Tag1AFThreshold = 0.05
)
Functions ¶
func AddClnsigConf ¶ added in v2.11.0
func AddTier ¶
func AddTier(item map[string]string, stats map[string]int, geneList, specVarDb map[string]bool, isTrio, isWGS, allGene bool, AFlist []string)
AddTier add tier to item
func ExonPrimer ¶ added in v2.15.0
ExonPrimer return 引物设计 for exon cnv
func GetFromMultiKeys ¶ added in v2.19.0
func GetFromMultiKeys(db map[string]map[string]string, keys []string) (info map[string]string, hit bool)
GetFromMultiKeys loop keys, return info,hit
func InheritCheck ¶
InheritCheck count variants of gene
func InheritCoincide ¶
func InheritCoincide(item map[string]string, inheritDb map[string]map[string]int, isTrio bool) string
InheritCoincide calculate 遗传相符
func InheritFrom ¶
InheritFrom return 变异来源
func InheritFrom2 ¶
InheritFrom2 for no strand proband-father-mother return 变异来源
func LargePrimer ¶ added in v2.15.0
LargePrimer return 引物设计 for large cnv
func LoadGeneTrans ¶
func LoadGeneTrans(fileName string)
LoadGeneTrans read geneSymbol.transcript.txt to two map
func ParseSpliceAI ¶ added in v2.5.1
ParseSpliceAI parse and anno spliceAI result
func UpdateAutoRule ¶
UpdateAutoRule update auto rules of acmg2015
func UpdateCnvAnnot ¶
func UpdateCnvAnnot(geneLst, key string, item, gene2id map[string]string, geneDisDb map[string]map[string]string)
UpdateCnvAnnot update annot of cnv
func UpdateDisGenes ¶
func UpdateDisGenes( sep string, genes []string, item, gene2id, geneDisDbCol map[string]string, geneDisDb map[string]map[string]string)
UpdateDisGenes add gene-disease info to item
func UpdateDisease ¶
func UpdateDisease(geneID string, item, gDiseaseDbColumn map[string]string, gDiseaseDbs map[string]map[string]string)
UpdateDisease add disease info to item
func UpdateFuncRegion ¶
UpdateFuncRegion Convert C* to CDS*
func UpdateFunction ¶
UpdateFunction convert intron to [splice+10,splice-10,splice+20,splice-20]
func UpdateGeneDb ¶ added in v2.8.0
UpdateGeneDb annotate 突变频谱
func UpdateManualRule ¶
UpdateManualRule update manualRuleName and manualExplaination
func UpdateRedis ¶
UpdateRedis update item from redis
func UpdateSnvTier1 ¶
UpdateSnvTier1 add other info for tier1 variant
func UpdateTags ¶
UpdateTags get Tags of item
func UpdateZygosity ¶ added in v2.9.8
UpdateZygosity format, fix hom and fix hemi
func ZygosityFormat ¶ added in v2.17.4
Types ¶
type AnnoDb ¶ added in v2.8.0
type AnnoDb struct {
File string
MainKey string
TitleKey []string
Title []string
// contains filtered or unexported fields
}
type EncodeDb ¶ added in v2.8.0
type EncodeDb struct {
File string
MainKey string
TitleKey []string
Title []string
Db map[string]map[string]string
// contains filtered or unexported fields
}
EncodeDb encode json
func (*EncodeDb) AnnoMultiKey ¶ added in v2.20.0
Source Files
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