lib

package

v0.0.0-...-32ad967 Latest Latest Go to latest Published: Mar 12, 2024 License: Apache-2.0 Imports: 13 Imported by: 0

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Repository

github.com/cdiener/architeuthis

Links

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Documentation ¶

Index ¶

func AddLineage[K any](taxids map[string]K, data_dir string, format string) map[string]*Lineage
func Confidence(abundances map[string]uint32, classification string) float64
func Entropy(abundances map[string]uint32) float64
func FilterReads(k2path string, out string, data_dir string, format string, ...) error
func GetFormat(filename string) (string, bool)
func GetLeaf(lin *Lineage) (int, string)
func GetRanks(format string) []string
func HasTaxonkit() (string, bool)
func Multiplicity(abundances map[string]uint32) uint32
func ParseMapping(k2map Mapping, line string) error
func SampleAppend(files []string, out string, sep rune) error
func SaveMapping(k2map Mapping, filepath string, sample_id string) error
func ScoreReadsToFile(k2path string, out string, data_dir string, format string) error
func SimpleAppend(files []string, out string) error
func TaxonDB(filepath string, data_dir string, format string) (map[string]*Lineage, int)
func UpdateMapping(entry *Taxon, kmer_taxid string, count int)
type Lineage
type Mapping
- func CollapseRanks(k2map Mapping, data_dir string, format string) Mapping
- func SummarizeKmers(filepath string) (Mapping, error)
type ReadScore
- func ScoreRead(line string, taxondb map[string]*Lineage) *ReadScore
type Taxon

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func AddLineage ¶

func AddLineage[K any](taxids map[string]K, data_dir string, format string) map[string]*Lineage

func Confidence ¶

func Confidence(abundances map[string]uint32, classification string) float64

func Entropy ¶

func Entropy(abundances map[string]uint32) float64

func FilterReads ¶

func FilterReads(k2path string, out string, data_dir string,
	format string, min_consistency float64, max_entropy float64, max_multiplicity uint32) error

func GetFormat ¶

func GetFormat(filename string) (string, bool)

func GetLeaf ¶

func GetLeaf(lin *Lineage) (int, string)

func GetRanks ¶

func GetRanks(format string) []string

func HasTaxonkit ¶

func HasTaxonkit() (string, bool)

func Multiplicity ¶

func Multiplicity(abundances map[string]uint32) uint32

func ParseMapping ¶

func ParseMapping(k2map Mapping, line string) error

func SampleAppend ¶

func SampleAppend(files []string, out string, sep rune) error

func SaveMapping ¶

func SaveMapping(k2map Mapping, filepath string, sample_id string) error

func ScoreReadsToFile ¶

func ScoreReadsToFile(k2path string, out string, data_dir string, format string) error

func SimpleAppend ¶

func SimpleAppend(files []string, out string) error

func TaxonDB ¶

func TaxonDB(filepath string, data_dir string, format string) (map[string]*Lineage, int)

func UpdateMapping ¶

func UpdateMapping(entry *Taxon, kmer_taxid string, count int)

Types ¶

type Lineage ¶

type Lineage struct {
	Names  []string
	Taxids []string
}

type Mapping ¶

type Mapping map[string]*Taxon

func CollapseRanks ¶

func CollapseRanks(k2map Mapping, data_dir string, format string) Mapping

func SummarizeKmers ¶

func SummarizeKmers(filepath string) (Mapping, error)

Summarize combines

type ReadScore ¶

type ReadScore struct {
	TaxonName    string
	TaxonID      uint32
	ID           string
	Kmers        uint32
	Consistency  float64
	Confidence   float64
	Multiplicity uint32
	Entropy      float64
}

func ScoreRead ¶

func ScoreRead(line string, taxondb map[string]*Lineage) *ReadScore

type Taxon ¶

type Taxon struct {
	Lineage string
	Reads   int
	Classes map[string]int
}

Source Files ¶

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