anno

package

v2.1.1 Latest Latest Go to latest Published: Sep 10, 2020 License: GPL-3.0 Imports: 16 Imported by: 2

Details

Valid go.mod file
Redistributable license
Tagged version
Stable version
Learn more about best practices

Repository

github.com/liserjrqlxue/anno2xlsx

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Open Source Insights

Documentation ¶

Index ¶

Variables
func AddTier(item map[string]string, stats map[string]int, ...)
func AnnoSpliceAI(item map[string]string)
func CnvPrimer(item map[string]string, cnvType string) (primer 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 GetNativeIndelField(item map[string]string) string
func GetNativeSnpField(item map[string]string) string
func GetPath(key, dbPath string, config map[string]interface{}) (path string)
func GetStrVal(key string, config map[string]interface{}) (val 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 LoadGeneTrans(fileName string)
func NewlineFormat(item map[string]string)
func Nm2Ensp(item map[string]string, db *redis.Client) error
func PrimerDesign(item map[string]string) string
func RedisNativeIndelAF(item map[string]string, db *redis.Client, key, field string) error
func RedisNativeSnpAF(item map[string]string, db *redis.Client, key, field string) error
func Score2Pred(item map[string]string)
func UpdateAutoRule(item map[string]string)
func UpdateCnvAnnot(geneLst string, item map[string]string, geneDisDb map[string]map[string]string)
func UpdateDisGenes(sep string, genes []string, item, geneDisDbCol map[string]string, ...)
func UpdateDiseMultiGene(geneLst string, item, geneDisDbCol map[string]string, ...)
func UpdateDisease(gene string, item, gDiseaseDbColumn map[string]string, ...)
func UpdateFuncRegion(item map[string]string)
func UpdateFunction(item 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, debug bool)
func UpdateSnvTier1(item map[string]string)
func UpdateTags(item map[string]string, specVarDb map[string]bool, isTrio bool) string
type GeneInfo
type OmimDisease
type SpliceAI
- func (ai *SpliceAI) Interpreatation(chromesome string, position int) (err error)
- func (ai *SpliceAI) Parse() (err error)

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	Gene2trans = make(map[string]string)
	Trans2gene = make(map[string]string)
)

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 AutoRuleKey = []string{
	"PVS1", "PS1", "PS4", "PM1", "PM2", "PM4", "PM5", "PP2", "PP3", "PP5", "BA1",
	"BS1", "BS2", "BP1", "BP3", "BP4", "BP6", "BP7",
}

View Source

var FuncInfo = map[string]int{
	"splice-3":     3,
	"splice-5":     3,
	"init-loss":    3,
	"alt-start":    3,
	"frameshift":   3,
	"nonsense":     3,
	"stop-gain":    3,
	"stop-loss":    2,
	"span":         3,
	"missense":     2,
	"cds-del":      2,
	"cds-indel":    2,
	"cds-ins":      2,
	"splice-10":    2,
	"splice+10":    2,
	"coding-synon": 1,
	"splice-20":    1,
	"splice+20":    1,
}

Tier1 >1 LoF 3

View Source

var ManualRuleKey = []string{
	"PVS1", "PS1", "PM5", "PS2", "PS3", "PM3", "PM6", "PP1",
	"PP4", "BS3", "BS4", "BP2", "BP5",
}

Functions ¶

func AddTier ¶

func AddTier(item map[string]string, stats map[string]int, geneList, specVarDb map[string]bool, isTrio, isWGS, allGene bool, AFlist []string)

add Tier to item

func AnnoSpliceAI ¶

func AnnoSpliceAI(item map[string]string)

func CnvPrimer ¶

func CnvPrimer(item map[string]string, cnvType string) (primer string)

CnvPrimer return 引物设计 for cnv

func FamilyTag ¶

func FamilyTag(item map[string]string, inheritDb map[string]map[string]int, tag string) string

FamilyTag return familyTag

func FloatFormat ¶

func FloatFormat(item map[string]string)

FloatFormat warp strconv.FormatFloat

func Format ¶

func Format(item map[string]string)

func GetNativeIndelField ¶

func GetNativeIndelField(item map[string]string) string

func GetNativeSnpField ¶

func GetNativeSnpField(item map[string]string) string

func GetPath ¶

func GetPath(key, dbPath string, config map[string]interface{}) (path string)

func GetStrVal ¶

func GetStrVal(key string, config map[string]interface{}) (val string)

func InheritCheck ¶

func InheritCheck(item map[string]string, inheritDb map[string]map[string]int)

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 ¶

func InheritFrom(item map[string]string, sampleList []string) string

InheritFrom return 变异来源

func InheritFrom2 ¶

func InheritFrom2(item map[string]string, sampleList []string) string

InheritFrom2 for no strand proband-father-mother return 变异来源

func LoadGeneTrans ¶

func LoadGeneTrans(fileName string)

LoadGeneTrans read geneSymbol.transcript.txt to two map

func NewlineFormat ¶

func NewlineFormat(item map[string]string)

NewlineForamt warp strings.Replace

func Nm2Ensp ¶

func Nm2Ensp(item map[string]string, db *redis.Client) error

func PrimerDesign ¶

func PrimerDesign(item map[string]string) string

PrimerDesign return 引物设计

func RedisNativeIndelAF ¶

func RedisNativeIndelAF(item map[string]string, db *redis.Client, key, field string) error

func RedisNativeSnpAF ¶

func RedisNativeSnpAF(item map[string]string, db *redis.Client, key, field string) error

func Score2Pred ¶

func Score2Pred(item map[string]string)

Score2Pred add _pred for scores

func UpdateAutoRule ¶

func UpdateAutoRule(item map[string]string)

func UpdateCnvAnnot ¶

func UpdateCnvAnnot(geneLst string, item map[string]string, geneDisDb map[string]map[string]string)

func UpdateDisGenes ¶

func UpdateDisGenes(
	sep string, genes []string,
	item, geneDisDbCol map[string]string,
	geneDisDb map[string]map[string]string)

UpdateDisGenes add gene-disease info to item

func UpdateDiseMultiGene ¶

func UpdateDiseMultiGene(geneLst string, item, geneDisDbCol map[string]string, geneDisDb map[string]map[string]string)

UpdateDiseMultiGene anno disease info for multil gene

func UpdateDisease ¶

func UpdateDisease(gene string, item, gDiseaseDbColumn map[string]string, geneDiseaseDb map[string]map[string]string)

UpdateDisease add disease info to item

func UpdateFuncRegion ¶

func UpdateFuncRegion(item map[string]string)

UpdateFuncRegion Convert C* to CDS*

func UpdateFunction ¶

func UpdateFunction(item map[string]string)

UpdateFunction fix splice+-20, have not implement

func UpdateManualRule ¶

func UpdateManualRule(item map[string]string)

func UpdateRedis ¶

func UpdateRedis(item map[string]string, db *redis.Client, keyPrefix string)

func UpdateSnv ¶

func UpdateSnv(item map[string]string, gender string, debug bool)

UpdateSnv add info for all variant

func UpdateSnvTier1 ¶

func UpdateSnvTier1(item map[string]string)

UpdateSnvTier1 add other info for tier1 variant

func UpdateTags ¶

func UpdateTags(item map[string]string, specVarDb map[string]bool, isTrio bool) string

UpdateTags return 筛选标签

Types ¶

type GeneInfo ¶

type GeneInfo struct {
	OmimGene     string        `json:"omimGene"`
	Transcript   string        `json:"transcript"`
	Exon         string        `json:"exon"`
	EffectType   string        `json:"effecttype"`
	Chr          string        `json:"chr"`
	Start        string        `json:"start"`
	Stop         string        `json:"stop"`
	Primer       string        `json:"primer"`
	OmimGeneId   string        `json:"omimGeneId"`
	Location     string        `json:"location"`
	OmimDiseases []OmimDisease `json:"omimDiseases"`
}

type OmimDisease ¶

type OmimDisease struct {
	DiseaseCnName    string `json:"diseaseCnName"`
	DiseaseEnName    string `json:"diseaseEnName"`
	GeneralizationCn string `json:"generalizationCn"`
	GeneralizationEn string `json:"generalizationEn"`
	OmimDiseaseId    string `json:"omimDiseaseId"`
	OmimGeneId       string `json:"omimGeneId"`
	SystemSort       string `json:"systemSort"`
	HeredityModel    string `json:"heredityModel"`
}

type SpliceAI ¶

type SpliceAI struct {
	SpliceAI, SpliceAI_Pred, SpliceAI_Interpretation, ALLELE, SYMBOL string
	DS_AG, DS_AL, DS_DG, DS_DL, DS_Max                               float64
	DP_AG, DP_AL, DP_DG, DP_DL                                       int
}

func (*SpliceAI) Interpreatation ¶

func (ai *SpliceAI) Interpreatation(chromesome string, position int) (err error)

func (*SpliceAI) Parse ¶

func (ai *SpliceAI) Parse() (err error)

Source Files ¶

View all Source files

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