evidence

package

v1.2.0 Latest Latest Go to latest Published: Apr 16, 2024 License: GPL-3.0 Imports: 15 Imported by: 0

Details

Valid go.mod file

The Go module system was introduced in Go 1.11 and is the official dependency management solution for Go.
Redistributable license

Redistributable licenses place minimal restrictions on how software can be used, modified, and redistributed.
Tagged version

Modules with tagged versions give importers more predictable builds.
Stable version

When a project reaches major version v1 it is considered stable.
Learn more about best practices

Repository

github.com/Ben-GO-package/acmg2015

Links

Open Source Insights

Documentation ¶

Index ¶

Variables
func CheckAFAllLowThen(item map[string]string, AFlist []string, threshold float64, includeEqual bool) bool
func CheckBA1(item map[string]string) string
func CheckBP1(item map[string]string) string
func CheckBP3(item map[string]string) string
func CheckBP4(item map[string]string) string
func CheckBP7(item map[string]string) string
func CheckBS1(item map[string]string) string
func CheckBS2(item map[string]string) string
func CheckDomain(item map[string]string) bool
func CheckOtherPathogenic(tbx *bix.Bix, item map[string]string, regions []Region) bool
func CheckPM1(item map[string]string, tbx *bix.Bix) string
func CheckPM2(item map[string]string) string
func CheckPM4(item map[string]string) string
func CheckPM5(item map[string]string) string
func CheckPP2(item map[string]string) string
func CheckPP3(item map[string]string, autoPVS1 bool) string
func CheckPS1(item map[string]string) string
func CheckPS4(item map[string]string) string
func CheckPVS1(item map[string]string, LOFList map[string]int, ...) string
func CompareBA1(item map[string]string, lostOnly bool)
func CompareBP1(item map[string]string, ClinVarBP1GeneList, HgmdBP1GeneList map[string]float64)
func CompareBP3(item map[string]string)
func CompareBP4(item map[string]string, lostOnly bool)
func CompareBP7(item map[string]string, lostOnly bool)
func CompareBS1(item map[string]string, lostOnly bool)
func CompareBS2(item map[string]string)
func ComparePM1(item map[string]string, tbx *bix.Bix)
func ComparePM2(item map[string]string)
func ComparePM4(item map[string]string)
func ComparePM5(item map[string]string, ...)
func ComparePP2(item map[string]string)
func ComparePP3(item map[string]string, lostOnly, autoPVS1 bool)
func ComparePS1(item map[string]string, ...)
func ComparePS4(item map[string]string)
func ComparePVS1(item map[string]string, LOFList map[string]int, ...)
func FindLOFIntoleranceGeneList(fileName, key string, pathogenicRegexp *regexp.Regexp) map[string]int
func FindPathogenicMissense(fileName, key string, pathogenicRegexp *regexp.Regexp) (map[string]int, map[string]int, map[string]int)
func LoadBA1(fileName string)
func LoadBP1(bp1geneList string)
func LoadBS2(fileName string)
func LoadLOF(LOFGeneListFile string) map[string]int
func LoadPM1(pfamId, interproDomain string)
func LoadPP2(fileName string)
func LoadPS1PM5(hgvs, pHgvs, aaPos string)
func PrintConflict(item map[string]string, rule, val string, keys ...string)
type Region

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	BS2LateOnsetHomoThreshold = 5
	BS2NoLateOnsetThreshold   = 0
	BS2HitCountThreshold      = 2
)

View Source

var (
	PM2ARAFThreshold  = 0.005
	PM2ADAFThreshold  = 0.0
	PM2ADAFThreshold2 = 0.00001
)

View Source

var (
	PM1Function = regexp.MustCompile(`missense|cds-indel`)

	IsClinVarPLP = regexp.MustCompile(`Pathogenic|Likely_pathogenic`)
	IsHgmdDM     = regexp.MustCompile(`DM$|DM\|`)
)

View Source

var BA1AFList = []string{
	"ESP6500 AF",
	"1000G AF",
	"ExAC AF",
	"GnomAD AF",
	"ExAC EAS AF",
	"GnomAD EAS AF",
}

View Source

var BA1AFThreshold = 0.05

View Source

var BS1AFList = []string{
	"1000G AF",
	"ExAC AF",
	"GnomAD AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"GnomAD EAS AF",
}

View Source

var BS1MorbidityThreshold = 0.01

View Source

var BS2AF1List = []string{
	"GnomAD EAS AF",
	"GnomAD AF",
	"1000G AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"ExAC AF",
}

View Source

var BS2HomoList = []string{
	"ExAC HomoAlt Count",
	"GnomAD HomoAlt Count",
}

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,
	"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 (
	LOFGeneList = make(map[string]int)
)

View Source

var PM2AFList = []string{
	"ESP6500 AF",
	"1000G AF",
	"ExAC AF",
	"ExAC EAS AF",
	"GnomAD AF",
	"GnomAD EAS AF",
}

View Source

var PS4GWASdbORThreshold = 5.0

View Source

var PVS1AFThreshold = 0.05

View Source

var PVS1AFlist = []string{
	"GnomAD EAS AF",
	"GnomAD AF",
	"1000G AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"ExAC AF",
}

Functions ¶

func CheckAFAllLowThen ¶

func CheckAFAllLowThen(item map[string]string, AFlist []string, threshold float64, includeEqual bool) bool

func CheckBA1 ¶

func CheckBA1(item map[string]string) string

ture : "1" flase: "0"

func CheckBP1 ¶

func CheckBP1(item map[string]string) string

BP1

func CheckBP3 ¶

func CheckBP3(item map[string]string) string

ture : "1" flase: "0"

func CheckBP4 ¶

func CheckBP4(item map[string]string) string

ture : "1" flase: "0"

func CheckBP7 ¶

func CheckBP7(item map[string]string) string

ture : "1" flase: "0"

func CheckBS1 ¶

func CheckBS1(item map[string]string) string

ture : "1" flase: "0"

func CheckBS2 ¶

func CheckBS2(item map[string]string) string

func CheckDomain ¶

func CheckDomain(item map[string]string) bool

突变位点后有重要的蛋白结构功能区域

func CheckOtherPathogenic ¶

func CheckOtherPathogenic(tbx *bix.Bix, item map[string]string, regions []Region) bool

突变位点后有其他致病突变（基于公共数据库）位点

func CheckPM1 ¶

func CheckPM1(item map[string]string, tbx *bix.Bix) string

PM1

func CheckPM2 ¶

func CheckPM2(item map[string]string) string

PM2

func CheckPM4 ¶

func CheckPM4(item map[string]string) string

ture : "1" flase: "0" nil : ""

func CheckPM5 ¶

func CheckPM5(item map[string]string) string

PM5

func CheckPP2 ¶

func CheckPP2(item map[string]string) string

PP2

func CheckPP3 ¶

func CheckPP3(item map[string]string, autoPVS1 bool) string

ture : "1" flase: "0"

func CheckPS1 ¶

func CheckPS1(item map[string]string) string

PS1

func CheckPS4 ¶

func CheckPS4(item map[string]string) string

ture : "1" flase: "0" nil : ""

func CheckPVS1 ¶

func CheckPVS1(item map[string]string, LOFList map[string]int, transcriptInfo map[string][]Region, tbx *bix.Bix) string

func CompareBA1 ¶

func CompareBA1(item map[string]string, lostOnly bool)

func CompareBP1 ¶

func CompareBP1(item map[string]string, ClinVarBP1GeneList, HgmdBP1GeneList map[string]float64)

func CompareBP3 ¶

func CompareBP3(item map[string]string)

func CompareBP4 ¶

func CompareBP4(item map[string]string, lostOnly bool)

func CompareBP7 ¶

func CompareBP7(item map[string]string, lostOnly bool)

func CompareBS1 ¶

func CompareBS1(item map[string]string, lostOnly bool)

func CompareBS2 ¶

func CompareBS2(item map[string]string)

func ComparePM1 ¶

func ComparePM1(item map[string]string, tbx *bix.Bix)

func ComparePM2 ¶

func ComparePM2(item map[string]string)

func ComparePM4 ¶

func ComparePM4(item map[string]string)

func ComparePM5 ¶

func ComparePM5(item map[string]string, ClinVarPHGVSlist, ClinVarAAPosList, HGMDPHGVSlist, HGMDAAPosList map[string]int)

func ComparePP2 ¶

func ComparePP2(item map[string]string)

func ComparePP3 ¶

func ComparePP3(item map[string]string, lostOnly, autoPVS1 bool)

func ComparePS1 ¶

func ComparePS1(item map[string]string, ClinVarMissense, ClinVarPHGVSlist, HGMDMissense, HGMDPHGVSlist map[string]int)

func ComparePS4 ¶

func ComparePS4(item map[string]string)

func ComparePVS1 ¶

func ComparePVS1(item map[string]string, LOFList map[string]int, transcriptInfo map[string][]Region, tbx *bix.Bix)

func FindLOFIntoleranceGeneList ¶

func FindLOFIntoleranceGeneList(fileName, key string, pathogenicRegexp *regexp.Regexp) map[string]int

func FindPathogenicMissense ¶

func FindPathogenicMissense(fileName, key string, pathogenicRegexp *regexp.Regexp) (map[string]int, map[string]int, map[string]int)

func LoadBA1 ¶

func LoadBA1(fileName string)

func LoadBP1 ¶

func LoadBP1(bp1geneList string)

func LoadBS2 ¶

func LoadBS2(fileName string)

func LoadLOF ¶ added in v1.2.0

func LoadLOF(LOFGeneListFile string) map[string]int

func LoadPM1 ¶

func LoadPM1(pfamId, interproDomain string)

func LoadPP2 ¶

func LoadPP2(fileName string)

func LoadPS1PM5 ¶

func LoadPS1PM5(hgvs, pHgvs, aaPos string)

func PrintConflict ¶

func PrintConflict(item map[string]string, rule, val string, keys ...string)

Types ¶

type Region ¶

type Region struct {
	Seqid string
	//Source string
	Type       string
	Chromosome string
	Start      uint64
	End        uint64
	Strand     string
	Gene       string
}

Source Files ¶

View all Source files

?	: This menu
/	: Search site
f or F	: Jump to
y or Y	: Canonical URL