pathways

Documentation

Index

• func ConnectDB() (*sqlx.DB, error)
• func GetDNA(pathways []pathdata, levels int) (map[string][]DNA, error)
• func GetTotalPathways(target_molecule string, levels int) ([]pathdata, error)
• func LoadSQLFile(path string) (string, error)
• func NameToId(name string) (int, error)
• func OrganismFilteredPathways(GBOrganism string, target_molecule string, levels int) ([]pathdata, error)
• type DNA

Functions

func ConnectDB

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

Easy database connector

func GetDNA

func GetDNA(pathways []pathdata, levels int) (map[string][]DNA, error)

func GetTotalPathways

func GetTotalPathways(target_molecule string, levels int) ([]pathdata, error)

Recursively searches throughout the database and fetches the pathways that lead to your target compound. This query excludes any compound that occurs more than 100 times in nodes. That parameter can change, but once we start including things like NADPH, ATP, H2O, we step into combinatorial explosions. id_path shows you the chain of equations starting from the top, and path shows you the actual compoounds that build up a path, which is usually just the most significant reactants and products.

func LoadSQLFile

func LoadSQLFile(path string) (string, error)

Reads and loads SQL files as string

func NameToId

func NameToId(name string) (int, error)

Gets id from compound name if it exists in ark

func OrganismFilteredPathways

func OrganismFilteredPathways(GBOrganism string, target_molecule string, levels int) ([]pathdata, error)

GetTotalPathways but limited to a single organism

Types

type DNA

type DNA struct {
	Id                         int
	Sequence, Seqhash, Genbank string
}