blastm8

Documentation

Overview

Package blastm8 allows reading and parsing of m8-formatted blast files

Index

• func Procfile(iblast *bufio.Reader, queryChan chan<- *BlastBlock)
• type BlastBlock
  • func (b BlastBlock) String() string
• type Header
• type Hit
  • func (h *Hit) Bitsc() float64
  • func (h *Hit) GI() int
  • func (h Hit) String() string
• type Hits
  • func (h Hits) Len() int
  • func (h Hits) Less(i, j int) bool
  • func (h Hits) Swap(i, j int)
• type QueryRes
  • func ParseRecord(bb BlastBlock, scLim float64) *QueryRes
  • func (t QueryRes) String() string

Functions

func Procfile

func Procfile(iblast *bufio.Reader, queryChan chan<- *BlastBlock)

ProcFile reads the query results from a blast m8-formatted file and passes the results to the queryChan channel. What is passed is the raw block of lines corresponding to a single query in the blast file.

Types

type BlastBlock

type BlastBlock struct {
	// contains filtered or unexported fields
}

BlastBlock represents a block of Blast hits

func (BlastBlock) String

func (b BlastBlock) String() string

String stringify a BlastBlock

type Header

type Header []byte

Header represents a Query or Subject -- typical headers of nr/nt as they appear in blast-m8 results

type Hit

type Hit struct {
	// contains filtered or unexported fields
}

Hit gives single Blast hit information

func (*Hit) Bitsc

func (h *Hit) Bitsc() float64

Bitsc returns the bit score of the corresponding Hit

func (*Hit) GI

func (h *Hit) GI() int

GI returns the GI of the corresponding Hit

func (Hit) String

func (h Hit) String() string

String stringify a hit

type Hits

type Hits []*Hit

Hits represent a collection of hits

func (Hits) Len

func (h Hits) Len() int

Sort interface for Hits by bitscore

func (Hits) Less

func (h Hits) Less(i, j int) bool

Sort interface for Hits by bitscore

func (Hits) Swap

func (h Hits) Swap(i, j int)

Sort interface for Hits by bitscore

type QueryRes

type QueryRes struct {
	Query Header
	Hits  Hits
}

QueryRes has the needed information about the hits of a query

func ParseRecord

func ParseRecord(bb BlastBlock, scLim float64) *QueryRes

ParseRecord parses the lines for a query (blast m8-formatted) and write the information in a QueryRes Only the lines with bit score greater than the best score * scLim are processed

func (QueryRes) String

func (t QueryRes) String() string

String Stringifies a query result