data

Documentation

Index

• Constants
• Variables
• func GetProtID(symbol string) (string, error)
• func GetProtLength(accession string) (int, error)
• func GetProtMapping(dbname, geneid string) (string, error)
• type GraphicFeature
  • func GetPfamProteinMatches(accession string) ([]GraphicFeature, error)
  • func GetSequenceFeatures(accession string) ([]GraphicFeature, error)
• type GraphicMetadata
• type GraphicResponse
  • func GetLocalGraphicData(filename string) (*GraphicResponse, error)
• type InterProEntry
• type InterProEntryResponse
• type InterProExtraField
• type InterProFeature
• type InterProFragment
• type InterProLocation
• type InterProMatch
• type InterProMetaData
• type UniProtResponse
• type UniProtSequence

Constants

const PfamLink = "https://www.ebi.ac.uk/interpro/entry/pfam/%s"

const PfamURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/uniprot/%s/?extra_fields=short_name&page_size=100"

const SequenceFeaturesURL = "https://www.ebi.ac.uk/interpro/api/protein/UniProt/%s/?extra_features=true"

const UNIPROTRESTURL = "" /* 135-byte string literal not displayed */

Variables

var MotifNames = map[string]string{
	"disorder":       "Disordered region",
	"low_complexity": "Low complexity region",
	"sig_p":          "Signal peptide region",
	"coiled_coil":    "Coiled-coil motif",
	"transmembrane":  "Transmembrane region",
}

MotifNames has human-readable names

• mostly from http://pfam-legacy.xfam.org/help#tabview=tab9

Functions

func GetProtID

func GetProtID(symbol string) (string, error)

func GetProtLength

func GetProtLength(accession string) (int, error)

func GetProtMapping

func GetProtMapping(dbname, geneid string) (string, error)

Types

type GraphicFeature

type GraphicFeature struct {
	Color    string          `json:"colour"`
	Text     string          `json:"text"`
	Type     string          `json:"type"`
	Start    json.Number     `json:"start"`
	End      json.Number     `json:"end"`
	Link     string          `json:"href"`
	Metadata GraphicMetadata `json:"metadata"`
}

GraphicFeature is a generic representation of various feature responses

func GetPfamProteinMatches

func GetPfamProteinMatches(accession string) ([]GraphicFeature, error)

func GetSequenceFeatures

func GetSequenceFeatures(accession string) ([]GraphicFeature, error)

type GraphicMetadata

type GraphicMetadata struct {
	Description string `json:"description"`
	Identifier  string `json:"identifier"`
}

type GraphicResponse

type GraphicResponse struct {
	Length   json.Number      `json:"length"`
	Metadata GraphicMetadata  `json:"metadata"`
	Motifs   []GraphicFeature `json:"motifs"`
	Regions  []GraphicFeature `json:"regions"`
}

func GetLocalGraphicData

func GetLocalGraphicData(filename string) (*GraphicResponse, error)

type InterProEntry

type InterProEntry struct {
	Metadata    InterProMetaData   `json:"metadata"`
	Matches     []InterProMatch    `json:"proteins"`
	ExtraFields InterProExtraField `json:"extra_fields"`
}

type InterProEntryResponse

type InterProEntryResponse struct {
	Entries []InterProEntry `json:"results"`
}

type InterProExtraField

type InterProExtraField struct {
	ShortName string `json:"short_name"`
}

type InterProFeature

type InterProFeature struct {
	Accession string             `json:"accession"`
	Database  string             `json:"source_database"`
	Locations []InterProLocation `json:"locations"`
}

type InterProFragment

type InterProFragment struct {
	Start      json.Number `json:"start"`
	End        json.Number `json:"end"`
	SeqFeature string      `json:"seq_feature"`
}

type InterProLocation

type InterProLocation struct {
	Fragments []InterProFragment `json:"fragments"`
}

type InterProMatch

type InterProMatch struct {
	Locations []InterProLocation `json:"entry_protein_locations"`
}

type InterProMetaData

type InterProMetaData struct {
	Accession string `json:"accession"`
	Name      string `json:"name"`
	Type      string `json:"type"`
}

type UniProtResponse

type UniProtResponse struct {
	Sequence UniProtSequence `json:"sequence"`
}

type UniProtSequence

type UniProtSequence struct {
	Length int `json:"length"`
}