ensembl

package
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Published: Oct 30, 2022 License: MIT Imports: 2 Imported by: 0

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Constants

This section is empty.

Variables

This section is empty.

Functions

func Connect

func Connect() (*sqlx.DB, error)

Connects hangles the connection to the public Ensembl MySQL database

Types

type Exon

type Exon struct {
	HGNCAccession       string `db:"hgnc_accession"`
	GeneAccession       string `db:"gene_accession"`
	GeneName            string `db:"gene_name"`
	GeneDescription     string `db:"gene_description"`
	TranscriptAccession string `db:"transcript_accession"`
	RefSeqAccession     string `db:"refseq_accession"`
	Chromosome          string `db:"chromosome"`
	ExonNumber          uint   `db:"exon_number"`
	Strand              int    `db:"strand"`
	Start               uint64 `db:"start"`
	End                 uint64 `db:"end"`
	ExonAccession       string `db:"exon_accession"`
}

Exon represents a single row returned from the associated Ensembl query.

func GetExons

func GetExons(db *sqlx.DB) ([]Exon, error)

GetExons retrieves all GHCh38 exons from Ensembl.

type Synonym

type Synonym struct {
	GeneName string `db:"gene_name"`
	Synonym  string `db:"synonym"`
}

Synonym represents a single row returned from the associated Ensembl query.

func GetSynonyms

func GetSynonyms(db *sqlx.DB, HGNCname string) ([]Synonym, error)

GetSynonyms retrieves all gene synonyms from Ensembl given a canonical HGNC gene name.

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