taxdump

Nov 8, 2021

Changes in this version

+ var ErrIllegalColumnIndex = errors.New("unikmer: illegal column index, positive integer needed")

+ var ErrNamesNotLoaded = errors.New("unikmer: taxonomy names not loaded, please call: LoadNames")

+ var ErrRankNotLoaded = errors.New("unikmer: taxonomic ranks not loaded, please call: NewTaxonomyWithRank")

+ var ErrTooManyRanks = errors.New("unikmer: number of ranks exceed limit of 255")

+ var ErrUnkownRank = errors.New("unikmer: unknown rank")

+ type Taxonomy struct

+ DelNodes map[uint32]struct{}

+ MergeNodes map[uint32]uint32

+ Names map[uint32]string

+ Nodes map[uint32]uint32

+ Ranks map[string]interface{}

+ func NewTaxonomy(file string, childColumn int, parentColumn int) (*Taxonomy, error)

+ func NewTaxonomyFromNCBI(file string) (*Taxonomy, error)

+ func NewTaxonomyWithRank(file string, childColumn int, parentColumn int, rankColumn int) (*Taxonomy, error)

+ func NewTaxonomyWithRankFromNCBI(file string) (*Taxonomy, error)

+ func (t *Taxonomy) AtOrBelowRank(taxid uint32, rank string) bool

+ func (t *Taxonomy) CacheLCA()

+ func (t *Taxonomy) LCA(a uint32, b uint32) uint32

+ func (t *Taxonomy) LineageNames(taxid uint32) []string

+ func (t *Taxonomy) LineageTaxIds(taxid uint32) []uint32

+ func (t *Taxonomy) LoadDeletedNodes(file string, column int) error

+ func (t *Taxonomy) LoadDeletedNodesFromNCBI(file string) error

+ func (t *Taxonomy) LoadMergedNodes(file string, oldColumn int, newColumn int) error

+ func (t *Taxonomy) LoadMergedNodesFromNCBI(file string) error

+ func (t *Taxonomy) LoadNames(file string, taxidColumn int, nameColumn int, typeColumn int, _type string) error

+ func (t *Taxonomy) LoadNamesFromNCBI(file string) error

+ func (t *Taxonomy) MaxTaxid() uint32

+ func (t *Taxonomy) Name(taxid uint32) string

+ func (t *Taxonomy) Rank(taxid uint32) string

+ func (t *Taxonomy) TaxId(taxid uint32) (uint32, bool)