igem

package
v0.0.0-...-040724e Latest Latest
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This package is not in the latest version of its module.

 Go to latest Published: Jun 6, 2019 License: BSD-3-Clause, GPL-2.0, BSD-3-Clause, + 1 more Imports: 12 Imported by: 0

Documentation

Overview

Package for interacting with the iGem registry

Index

Constants

View Source 
const (
	GENERIC          = "BBa_B"
	PROTEINCODING    = "BBa_C"
	REPORTER         = "BBa_E"
	SIGNALLING       = "BBa_F"
	PRIMER           = "BBa_G"
	IAPPROJECT       = "BBa_I"
	IGEMPROJECT      = "BBa_J"
	TAG              = "BBa_M"
	PROTEINGENERATOR = "BBa_P"
	INVERTER         = "BBa_Q"
	REGULATORY       = "BBa_R"
	INTERMEDIATE     = "BBa_S"
	CELLSTRAIN       = "BBa_V"
)

Part Name classifications

BBa_B... = Generic basic parts such as Terminators, DNA, and Ribosome Binding Site BBa_C... = Protein coding parts BBa_E... = Reporter parts BBa_F... = Signalling parts BBa_G... = Primer parts BBa_I... = IAP 2003, 2004 project parts BBa_J... = iGEM project parts BBa_M... = Tag parts BBa_P... = Protein Generator parts BBa_Q... = Inverter parts BBa_R... = Regulatory parts BBa_S... = Intermediate parts BBa_V... = Cell strain parts

Variables

View Source 
var (
	IgemTypeCodes = map[string]string{
		"GENERIC":          "BBa_B",
		"PROTEINCODING":    "BBa_C",
		"REPORTER":         "BBa_E",
		"SIGNALLING":       "BBa_F",
		"PRIMER":           "BBa_G",
		"IAPPROJECT":       "BBa_I",
		"IGEMPROJECT":      "BBa_J",
		"TAG":              "BBa_M",
		"PROTEINGENERATOR": "BBa_P",
		"INVERTER":         "BBa_Q",
		"REGULATORY":       "BBa_R",
		"INTERMEDIATE":     "BBa_S",
		"CELLSTRAIN":       "BBa_V",
	}
)

Functions

func CountPartsinRegistryContaining 

func CountPartsinRegistryContaining(keystrings []string) (numberofparts int)

func FilterRegistry 

func FilterRegistry(partype string, keystrings []string, exacttypecodeonly bool) (listofpartIDs []string, idtodescriptionmap map[string]string, err error)

func GetDescription 

func GetDescription(partname string) (desc string)

func GetDescriptionfromSubset 

func GetDescriptionfromSubset(partname string, parsedxml Rsbpml) (desc string)

func GetRating 

func GetRating(partname string) (rating string)

func GetResults 

func GetResults(partname string) (results string)

func GetResultsfromSubset 

func GetResultsfromSubset(partname string, parsedxml Rsbpml) (results string)

change to object based method call

func GetSequence 

func GetSequence(partname string) (sequence string)

func GetType 

func GetType(partname string) (parttype string)

func MakeFastaURL 

func MakeFastaURL(partname string) (Urlstring string)

Types

type Categories 

type Categories struct {
	Categories []string `xml:"category"`
}

func GetCategories 

func GetCategories(partname string) (categories Categories)

type FastaPart 

type FastaPart struct {
	Part_id         string
	Desc            string
	Part_name       string
	Part_short_desc string
	Part_type       string
	Sample_status   string
	Seq_data        string
}

func Build_fasta 

func Build_fasta(header string, seq bytes.Buffer) (Record FastaPart)

func FastaParse 

func FastaParse(fastaFh io.Reader) []FastaPart

type IgemFeature 

type IgemFeature struct {
	Id        string `xml:"id"`
	Title     string `xml:"title"`
	Type      string `xml:"type"`
	Direction string `xml:"direction"`
	Startpos  string `xml:"startpos"`
	Endpos    string `xml:"endpos"`
}

type IgemFeatures 

type IgemFeatures struct {
	Features []IgemFeature `xml:"feature"`
}

type IgemParameter 

type IgemParameter struct {
	Name      string `xml:"name"`
	Value     string `xml:"value"`
	Units     string `xml:"units"`
	Url       string `xml:"url"`
	Id        string `xml:"id"`
	M_date    string `xml:"m_date"`
	User_id   string `xml:"user_id"`
	User_name string `xml:"user_name"`
}

type IgemParameters 

type IgemParameters struct {
	Parameters []IgemParameter `xml:"parameter"`
}

type Part 

type Part struct {
	Part_id            string         `xml:"part_id"`
	Part_name          string         `xml:"part_name"`
	Part_short_name    string         `xml:"part_short_name"`
	Part_short_desc    string         `xml:"part_short_desc"`
	Part_type          string         `xml:"part_type"`
	Release_status     string         `xml:"release_status"`
	Sample_status      string         `xml:"sample_status"`
	Part_results       string         `xml:"part_results"`
	Part_nickname      string         `xml:"part_nickname"`
	Part_rating        string         `xml:"part_rating"`
	Part_url           string         `xml:"part_url"`
	Part_entered       string         `xml:"part_entered"`
	Part_author        string         `xml:"part_author"`
	Deep_subparts      Subparts       `xml:"deep_subparts"`
	Specified_subparts Subparts       `xml:"specified_subparts"`
	Specified_subscars Subscars       `xml:"specified_subscars"`
	Sequencelist       []Sequence     `xml:"sequences"`
	Features           IgemFeatures   `xml:"features"`
	Parameters         IgemParameters `xml:"parameters"`
	Categories         Categories     `xml:"categories"`
	Twins              Twins          `xml:"twins"`
}

func GetPart 

func GetPart(partname string) (partproperties Part)

type Part_list 

type Part_list struct {
	Parts []Part `xml:"part"`
}

type Registryquerier 

type Registryquerier interface {
	GetParts([]string) []Rsbpml
}

type Rsbpml 

type Rsbpml struct {
	Partlist []Part_list `xml:"part_list"`
}

func FetchPartsXML 

func FetchPartsXML(parts []string) (parsedxml Rsbpml)

func LookUp 

func LookUp(parts []string) (parsedxml Rsbpml)

func ParseOutput 

func ParseOutput(xmldata []byte) (parsedxml Rsbpml)

func (*Rsbpml) Categories 

func (parsedxml *Rsbpml) Categories(partname string) (result Categories)

func (*Rsbpml) Description 

func (parsedxml *Rsbpml) Description(partname string) (result string)

func (*Rsbpml) Rating 

func (parsedxml *Rsbpml) Rating(partname string) (result string)

func (*Rsbpml) Results 

func (parsedxml *Rsbpml) Results(partname string) (result string)

func (*Rsbpml) Sequence 

func (parsedxml *Rsbpml) Sequence(partname string) (sequence string)

Add Get funcs to get data from Rsbpml? Would be much faster

func (*Rsbpml) Type 

func (parsedxml *Rsbpml) Type(partname string) (result string)

type Scar 

type Scar struct {
	Scar_id       string `xml:"scar_id"`
	Scar_standard string `xml:"scar_standard"`
	Scar_type     string `xml:"scar_type"`
	Scar_name     string `xml:"scar_name"`
	Scar_nickname string `xml:"scar_nickname"`
	Scar_comments string `xml:"scar_comments"`
	Scar_sequence string `xml:"scar_sequence"`
}

type Sequence 

type Sequence struct {
	Seq_data string `xml:"seq_data"`
}

type Subpart 

type Subpart struct {
	Part_id         string `xml:"part_id"`
	Part_name       string `xml:"part_name"`
	Part_short_desc string `xml:"part_short_desc"`
	Part_type       string `xml:"part_type"`
	Part_nickname   string `xml:"part_nickname"`
}

type Subparts 

type Subparts struct {
	Subparts []Subpart `xml:"subpart"`
}

type Subscars 

type Subscars struct {
	Subparts []Subpart `xml:"subpart"`
	Scars    []Scar    `xml:"scar"`
}

type Twins 

type Twins struct {
	Twins []string `xml:"twin"`
}

Source Files

View all Source files

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