blast

func AllExactMatches ¶

func AllExactMatches(hits []blast.Hit) (exactmatches []blast.Hit, summary string, err error)

func BLAST ¶

func BLAST(query string, p *blast.PutParameters) (o *blast.Output, err error)

BLAST performs a blast call for specified query parameters For parameters see https://github.com/biogo/ncbi/blob/master/blast/blast.go For documentation on settings see https://ncbi.github.io/blast-cloud/dev/api.html Commonly used parameters include

Program       string      BLAST program to use (e.g. "blastp", "blastn")
Database      string      Target database name (e.g. "nr", "refseq_rna", "pdb")
EntrezQuery   string      Entrez results filter (e.g. "Homo sapiens[organism]")
Expect        *float64    Expect threshold
HitListSize   int         Number of target sequences to return

func FindBestHit ¶

func FindBestHit(hits []blast.Hit) (besthit blast.Hit, identity float64, coverage float64, besthitsummary string, err error)

func HitSummary ¶

func HitSummary(hits []blast.Hit, topnumberofhits int, topnumberofhsps int) (summary string, err error)

func Hits ¶

func Hits(o *blast.Output) (hits []blast.Hit, err error)

func MegaBlastN ¶

func MegaBlastN(query string) (hits []blast.Hit, err error)

func MegaBlastP ¶

func MegaBlastP(query string) (hits []blast.Hit, err error)

func RerunRID ¶

func RerunRID(r *blast.Rid) (o *blast.Output, err error)

func RerunRIDstring ¶

func RerunRIDstring(rid string) (o *blast.Output, err error)

func SimpleBlast ¶

func SimpleBlast(query string) (*blast.Output, error)

SimpleBlast performs a blast call with pre-set query parameters