script

Documentation

Overview

Package script provides functions for downloading and processing REBASE files.

REBASE is a database of restriction enzymes and their recognition sites. The database is available for download at ftp://ftp.neb.com/pub/rebase.

The REBASE database is distributed as a set of files, each containing a different type of information. The files are named according to the following pattern:

emboss_e.###	- Enzyme names and recognition sites
emboss_s.###	- Enzyme suppliers
emboss_r.###	- Enzyme references
bairoch.###

where ### represents the REBASE version.

Index

• func CreateGoEnzymeDBFile(rebaseData *RebaseData, outputFilePath string) error
• func CreateGoEnzymeSupplierFile(rebaseData *RebaseData, outputFilePath string) error
• func RetrieveRebaseFiles(version string, downloadDir string) error
• func WriteEnzymeJSON(enzymes []enzyme.Enzyme, outputFilePath string) error
• type DBFileTemplateData
• type RebaseData
  • func ProcessRebaseFiles(rebaseInputDir, version string) (*RebaseData, error)
• type ReferenceRecord
• type SupplierFileTemplateData
• type SupplierRecord

Functions

func CreateGoEnzymeDBFile

func CreateGoEnzymeDBFile(rebaseData *RebaseData, outputFilePath string) error

func CreateGoEnzymeSupplierFile

func CreateGoEnzymeSupplierFile(rebaseData *RebaseData, outputFilePath string) error

func RetrieveRebaseFiles

func RetrieveRebaseFiles(version string, downloadDir string) error

func WriteEnzymeJSON

func WriteEnzymeJSON(enzymes []enzyme.Enzyme, outputFilePath string) error

Types

type DBFileTemplateData

type DBFileTemplateData struct {
	Enzymes string
}

type RebaseData

type RebaseData struct {
	Enzymes    map[string]enzyme.Enzyme
	Suppliers  map[string]string
	References map[string]ReferenceRecord
}

func ProcessRebaseFiles

func ProcessRebaseFiles(
	rebaseInputDir,
	version string,
) (*RebaseData, error)

type ReferenceRecord

type ReferenceRecord struct {
	EnzymeName    string
	Organism      string
	Isoschizomers string
	Methylation   string
	Source        string
	Suppliers     []string
	References    []string
}

type SupplierFileTemplateData

type SupplierFileTemplateData struct {
	Suppliers string
}

type SupplierRecord

type SupplierRecord struct {
	SupplierId   string
	SupplierName string
	Enzymes      []string
}