downloaddb

package

v0.6.0 Latest Latest Go to latest Published: Oct 27, 2021 License: Apache-2.0 Imports: 21 Imported by: 0

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Repository

github.com/zorino/kaamer

Links

Open Source Insights

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 ¶

View Source

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/"
)

View Source

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

Variables ¶

View Source

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

View Source

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

View Source

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,
	}
)

View Source

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"`
}

Source Files ¶

View all Source files

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