lib

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v0.0.0-...-95e9d17 Latest Latest Go to latest Published: Jan 29, 2026 License: Apache-2.0 Imports: 14 Imported by: 0

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Repository

github.com/cdiener/architeuthis

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Documentation ¶

Overview ¶

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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 CountLines(path string) (int, error)
func Entropy(abundances map[string]uint32) float64
func FilterReads(k2path string, out string, data_dir string, format string, named bool, ...) 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, named bool) 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, named bool) error
func SimpleAppend(files []string, out string, header bool) error
func TaxID(token string, named bool) string
func TaxonDB(filepath string, data_dir string, format string, named bool) (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, named bool) (Mapping, error)
type Node
type ReadScore
- func ScoreRead(line string, taxondb map[string]*Lineage, named bool) *ReadScore
type Taxon
type Tree

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 CountLines ¶

func CountLines(path string) (int, error)

Count the number of lines in a file

func Entropy ¶

func Entropy(abundances map[string]uint32) float64

func FilterReads ¶

func FilterReads(k2path string, out string, data_dir string,
	format string, named bool, 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, named bool) 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, named bool) error

func SimpleAppend ¶

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

func TaxID ¶

func TaxID(token string, named bool) string

func TaxonDB ¶

func TaxonDB(filepath string, data_dir string, format string, named bool) (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, named bool) (Mapping, error)

Summarize combines

type Node ¶

type Node struct {
	Taxid    int
	Name     string
	Parent   *Node
	Children []*Node
	Value    float64
}

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, named bool) *ReadScore

type Taxon ¶

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

type Tree ¶

type Tree struct {
	Root     *Node
	Taxids   map[int]*Node
	Children []*Node
}

Source Files ¶

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