downloaddb

Documentation

Index

• Constants
• Variables
• func DownloadBiocyc(dbPath string)
• func DownloadGenbankGenome(genomeId string)
• func DownloadKEGG(dbPath string)
• func DownloadRefseq(outputFile string, taxon string)
• func DownloadUniprot(outputFile string, taxon string)
• func GetBiocycPathway(id string) []string
• func GetKeggPathway(id string) []string
• func IODownloadFTP(dstFile *os.File, host string, path string)
• func IODownloadHTTP(dstFile *os.File, url string)
• func IOListFTP(host string, path string) []*ftp.Entry
• func ParseGenbank(gbkFile string)
• type Pathway
• type WriteCounter
  • func (wc WriteCounter) PrintProgress()
  • func (wc *WriteCounter) Write(p []byte) (int, error)
• type XMLRoot

Constants

const (
	NCBI_refseq_ftp_host = "ftp.ncbi.nlm.nih.gov:21"
	NCBI_refseq_ftp_path = "/refseq/release/"
	NCBI_eutil_api_path  = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
)

const (
	Uniprot_ftp_host           = "ftp.uniprot.org:21"
	Uniprot_ftp_taxonomic_path = "/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/"
)

Variables

var (
	BIOCYC_API = "https://websvc.biocyc.org"
)

var (
	KEGG_API = "http://rest.kegg.jp"
)

var (
	NCBI_refseq_valid = map[string]bool{
		"archaea":              true,
		"bacteria":             true,
		"fungi":                true,
		"invertebrate":         true,
		"mitochondrion":        true,
		"plant":                true,
		"plasmid":              true,
		"plastid":              true,
		"protozoa":             true,
		"viral":                true,
		"vertebrate_mammalian": true,
		"vertebrate_other":     true,
	}
)

var (
	Uniprot_ftp_taxonomic_valid = map[string]bool{
		"archaea":       true,
		"bacteria":      true,
		"fungi":         true,
		"human":         true,
		"invertebrates": true,
		"mammals":       true,
		"plants":        true,
		"rodents":       true,
		"vertebrates":   true,
		"viruses":       true,
	}
)

Functions

func DownloadBiocyc

func DownloadBiocyc(dbPath string)

func DownloadGenbankGenome

func DownloadGenbankGenome(genomeId string)

func DownloadKEGG

func DownloadKEGG(dbPath string)

func DownloadRefseq

func DownloadRefseq(outputFile string, taxon string)

func DownloadUniprot

func DownloadUniprot(outputFile string, taxon string)

func GetBiocycPathway

func GetBiocycPathway(id string) []string

func GetKeggPathway

func GetKeggPathway(id string) []string

func IODownloadFTP

func IODownloadFTP(dstFile *os.File, host string, path string)

func IODownloadHTTP

func IODownloadHTTP(dstFile *os.File, url string)

func IOListFTP

func IOListFTP(host string, path string) []*ftp.Entry

func ParseGenbank

func ParseGenbank(gbkFile string)

Types

type Pathway

type Pathway struct {
	XMLName xml.Name `xml:"Pathway"`
	ID      string   `xml:"ID,attr"`
	Name    string   `xml:"common-name"`
}

type WriteCounter

type WriteCounter struct {
	Total uint64
}

WriteCounter counts the number of bytes written to it. It implements to the io.Writer interface and we can pass this into io.TeeReader() which will report progress on each write cycle.

func (WriteCounter) PrintProgress

func (wc WriteCounter) PrintProgress()

func (*WriteCounter) Write

func (wc *WriteCounter) Write(p []byte) (int, error)

type XMLRoot

type XMLRoot struct {
	XMLName  xml.Name  `xml:"ptools-xml"`
	Version  xml.Attr  `xml:"ptools-version,attr"`
	Pathways []Pathway `xml:"Pathway"`
}