Usage
Construct Database
# Load the package
julia> using Taxonomy
# Construct a Taxonomy.DB object from the path to each file
julia> db = Taxonomy.DB("db/nodes.dmp","db/names.dmp")
Taxonomy.DB("db/nodes.dmp","db/names.dmp")
# Taxonomy.DB object is automatically stored in current_db()
julia> current_db()
Taxonomy.DB("db/nodes.dmp","db/names.dmp")Get taxonomic information from Taxon
# Construct a Taxon from taxid and Taxonomy.DB
julia> human = Taxon(9606, db)
9606 [species] Homo sapiens
# Or, you can omit db from argument (current_db() loaded)
julia> human = Taxon(9606)
9606 [species] Homo sapiens
julia> taxid(human)
9606
julia> name(human)
"Homo sapiens"
julia> rank(human)
:speciesConstruct Taxons from names
Name must match to the scientific name excatly
julia> ["Homo", "Viruses", "Drosophila"] .|> name2taxids |> Iterators.flatten .|> Taxon
5-element Vector{Taxon}:
9605 [genus] Homo
10239 [superkingdom] Viruses
7215 [genus] Drosophila
2081351 [genus] Drosophila
32281 [subgenus] DrosophilaTraverse taxonomic subtrees from a given Taxon
julia> children(human)
2-element Vector{Taxon}:
741158 [subspecies] Homo sapiens subsp. 'Denisova'
63221 [subspecies] Homo sapiens neanderthalensis
julia> AbstractTrees.parent(human)
9605 [genus] Homo
# Collect all Taxon in subtree using PreOderDFS iterator from AbstractTrees.jl
julia> collect(AbastractTrees.PreOrderDFS(human))
3-element Vector{Taxon}:
9606 [species] Homo sapiens
741158 [subspecies] Homo sapiens subsp. 'Denisova'
63221 [subspecies] Homo sapiens neanderthalensis
# Print subtree
julia> print_tree(Taxon(9604))
9604 [family] Hominidae
├─ 2922387 [no rank] unclassified Hominidae
│ └─ 2922388 [species] Hominidae sp.
├─ 607660 [subfamily] Ponginae
│ └─ 9599 [genus] Pongo
│ ├─ 502961 [species] Pongo abelii x pygmaeus
│ ├─ 9600 [species] Pongo pygmaeus
│ │ ├─ 9602 [subspecies] Pongo pygmaeus pygmaeus
│ │ ├─ 2753605 [subspecies] Pongo pygmaeus morio
│ │ └─ 2753606 [subspecies] Pongo pygmaeus wurmbii
│ ├─ 9601 [species] Pongo abelii
│ ├─ 2624844 [no rank] unclassified Pongo
│ │ └─ 9603 [species] Pongo sp.
│ └─ 2051901 [species] Pongo tapanuliensis
├─ 2883640 [no rank] Hominidae intergeneric hybrids
│ └─ 2883641 [species] Homo sapiens x Pan troglodytes tetraploid cell line
└─ 207598 [subfamily] Homininae
├─ 9596 [genus] Pan
│ ├─ 9597 [species] Pan paniscus
│ └─ 9598 [species] Pan troglodytes
│ ├─ 37011 [subspecies] Pan troglodytes troglodytes
│ ├─ 37010 [subspecies] Pan troglodytes schweinfurthii
│ ├─ 756884 [subspecies] Pan troglodytes ellioti
│ ├─ 1294088 [subspecies] Pan troglodytes verus x troglodytes
│ └─ 37012 [subspecies] Pan troglodytes verus
├─ 9605 [genus] Homo
│ ├─ 2665952 [no rank] environmental samples
│ │ └─ 2665953 [species] Homo sapiens environmental sample
│ ├─ 2813598 [no rank] unclassified Homo
│ │ └─ 2813599 [species] Homo sp.
│ ├─ 9606 [species] Homo sapiens
│ │ ├─ 741158 [subspecies] Homo sapiens subsp. 'Denisova'
│ │ └─ 63221 [subspecies] Homo sapiens neanderthalensis
│ └─ 1425170 [species] Homo heidelbergensis
└─ 9592 [genus] Gorilla
├─ 9593 [species] Gorilla gorilla
│ ├─ 183511 [subspecies] Gorilla gorilla uellensis
│ ├─ 406788 [subspecies] Gorilla gorilla diehli
│ └─ 9595 [subspecies] Gorilla gorilla gorilla
└─ 499232 [species] Gorilla beringei
├─ 46359 [subspecies] Gorilla beringei graueri
└─ 1159185 [subspecies] Gorilla beringei beringeiNote: Use the child-to-parent traverse (AbstrcatTrees.parent) as much as possible since it is quite faster than parent-to-child traverse (children and iterators from AbstractTrees.jl).
Find lowest common ancestor (LCA)
julia> human = Taxon(9606); gorilla = Taxon(9592); orangutan = Taxon(9600);
juliia> lca(human, gorilla)
207598 [subfamily] Homininae
# lca is a "varargs" function
julia> lca(human, gorilla, orangutan)
9604 [family] Hominidaes
# Vector input is also available
julia> lca([human, gorilla, orangutan])
9604 [family] HominidaeEvaluate ancestor-descendant relationships between two Taxons
julia> viruses = Taxon(10239)
10239 [superkingdom] Viruses
julia> sars_cov2 = Taxon(2697049)
2697049 [no rank] Severe acute respiratory syndrome coronavirus 2
julia> isancestor(viruses, sars_cov2)
true
julia> isdescendant(human, viruses)
falseFilter Taxons by a rank range
julia> taxa = [2759, 33208, 7711, 40674, 9443, 9604, 9605, 9606] .|> Taxon
8-element Vector{Taxon}:
2759 [superkingdom] Eukaryota
33208 [kingdom] Metazoa
7711 [phylum] Chordata
40674 [class] Mammalia
9443 [order] Primates
9604 [family] Hominidae
9605 [genus] Homo
9606 [species] Homo sapiens
# Filter Taxons lower than a given rank
julia> filter(taxa) do taxon
taxon < Rank(:class)
end
4-element Vector{Taxon}:
9443 [order] Primates
9604 [family] Hominidae
9605 [genus] Homo
9606 [species] Homo sapiens
julia> filter(taxa) do taxon
taxon <= Rank(:species)
end
1-element Vector{Taxon}:
9606 [species] Homo sapiensTreat taxonomic Lineage
julia> lineage = Lineage(human)
32-element Lineage{Taxon}:
1 [no Rank] root
131567 [no rank] cellular organisms
2759 [superkingdom] Eukaryota
33154 [clade] Opisthokonta
33208 [kingdom] Metazoa
6072 [clade] Eumetazoa
33213 [clade] Bilateria
33511 [clade] Deuterostomia
7711 [phylum] Chordata
⋮
9443 [order] Primates
376913 [suborder] Haplorrhini
314293 [infraorder] Simiiformes
9526 [parvorder] Catarrhini
314295 [superfamily] Hominoidea
9604 [family] Hominidae
207598 [subfamily] Homininae
9605 [genus] Homo
9606 [species] Homo sapiensTaxon information are stored in Vector-like format
julia> lineage[1]
1 [no Rank] root
julia> lineage[9]
7711 [phylum] Chordata
julia> lineage[end]
9606 [species] Homo sapiensSymbols such as :phylum, :genus and :species (Symbols in CanonicalRanks) are available to access each Taxon
julia> lineage[:phylum]
7711 [phylum] Chordata
julia> lineage[:genus]
9605 [genus] Homo
julia> lineage[:species]
9606 [species] Homo sapiensBetween, From, Until, Cols and All selectors are available in more complex rank selection scenarios.
julia> lineage[Between(:order, :family)]
6-element Lineage{Taxon}:
9443 [order] Primates
376913 [suborder] Haplorrhini
314293 [infraorder] Simiiformes
9526 [parvorder] Catarrhini
314295 [superfamily] Hominoidea
9604 [family] Hominidae
julia> lineage[From(:family)]
4-element Lineage{Taxon}:
9604 [family] Hominidae
207598 [subfamily] Homininae
9605 [genus] Homo
9606 [species] Homo sapiens
julia> lineage[Until(:kingdom)]
5-element Lineage{Taxon}:
1 [no Rank] root
131567 [no rank] cellular organisms
2759 [superkingdom] Eukaryota
33154 [clade] Opisthokonta
33208 [kingdom] Metazoa
julia> lineage[Cols(:superkingdom, :genus, :species)]
3-element Lineage{Taxon}:
2759 [superkingdom] Eukaryota
9605 [genus] Homo
9606 [species] Homo sapiensReformat Lineage
Reformation of Linage to your ranks can be performed by using reformat.
julia> seven_rank = [:superkingdom, :phylum, :class, :order, :family, :genus, :species];
julia> reformat(lineage, seven_rank)
7-element Lineage{Taxon}:
2759 [superkingdom] Eukaryota
7711 [phylum] Chordata
40674 [class] Mammalia
9443 [order] Primates
9604 [family] Hominidae
9605 [genus] Homo
9606 [species] Homo sapiensThe :subspecies/:strain are internally treated as the same rank, so that users can ignore ambiguities tn the rank below species.
julia> eight_rank = [:superkingdom, :phylum, :class, :order, :family, :genus, :species, :strain];
julia> denisova = Taxon(741158); l = Lineage(denisova);
julia> rl = reformat(l, eight_rank)
8-element Lineage{Taxon}:
2759 [superkingdom] Eukaryota
7711 [phylum] Chordata
40674 [class] Mammalia
9443 [order] Primates
9604 [family] Hominidae
9605 [genus] Homo
9606 [species] Homo sapiens
741158 [subspecies] Homo sapiens subsp. 'Denisova'
julia> rl[:subspecies] == rl[:strain]
trueIf there is no corresponding taxon to your ranks in the linneage, then UnclassifiedTaxon will be stored.
julia> uncultured_bacillales = Taxon(157472)
57472 [species] uncultured Bacillales bacterium
julia> reformatted_bacillales_lineage = reformat(Lineage(uncultured_bacillales), seven_rank)
7-element Lineage:
2 [superkingdom] Bacteria
1239 [phylum] Firmicutes
91061 [class] Bacilli
1385 [order] Bacillales
Unclassified [family] unclassified Bacillales family
Unclassified [genus] unclassified Bacillales genus
157472 [species] uncultured Bacillales bacteriumOnce reformatted, Lineage cannnot be reformatted again.
julia> isreformatted(reformatted_bacillales_lineage)
true
julia> reformat(reformatted_bacillales_lineage, seven_rank)
ERROR: It is already reformatted.
Stacktrace:
[1] _LR()
@ Taxonomy ~/.julia/dev/Taxonomy.jl/src/lineage.jl:7
[2] reformat(l::Lineage{Union{Taxon, UnclassifiedTaxon}}, ranks::Vector{Symbol})
@ Taxonomy ~/.julia/dev/Taxonomy.jl/src/lineage.jl:135
[3] top-level scope
@ REPL[103]:1Convert Lineages to DataFrame
Lineage can be converted to NamedTuple, using namedtuple.
Converted NamedTuple can be used as input into DataFrame
julia> using DataFrames
julia> seven_rank = [:superkingdom, :phylum, :class, :order, :family, :genus, :species];
julia> taxa = [9606, 562, 187878, 212035, 2697049] .|> Taxon
5-element Vector{Taxon}:
9606 [species] Homo sapiens
562 [species] Escherichia coli
187878 [species] Thermococcus gammatolerans
212035 [species] Acanthamoeba polyphaga mimivirus
2697049 [no rank] Severe acute respiratory syndrome coronavirus 2
julia> taxa .|> Lineage .|> (x -> reformat(x, seven_rank)) .|> namedtuple |> DataFrame
5×7 DataFrame
Row │ superkingdom phylum class order family genus species
│ Taxon Taxon Taxon Taxon Taxon Taxon Taxon
─────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2759 [superkingdom] Eukaryota 7711 [phylum] Chordata 40674 [class] Mammalia 9443 [order] Primates 9604 [family] Hominidae 9605 [genus] Homo 9606 [species] Homo sapiens
2 │ 2 [superkingdom] Bacteria 1224 [phylum] Proteobacteria 1236 [class] Gammaproteobacteria 91347 [order] Enterobacterales 543 [family] Enterobacteriaceae 561 [genus] Escherichia 562 [species] Escherichia coli
3 │ 2157 [superkingdom] Archaea 28890 [phylum] Euryarchaeota 183968 [class] Thermococci 2258 [order] Thermococcales 2259 [family] Thermococcaceae 2263 [genus] Thermococcus 187878 [species] Thermococcus ga…
4 │ 10239 [superkingdom] Viruses 2732007 [phylum] Nucleocytoviric… 2732523 [class] Megaviricetes 2732554 [order] Imitervirales 549779 [family] Mimiviridae 315393 [genus] Mimivirus 212035 [species] Acanthamoeba po…
5 │ 10239 [superkingdom] Viruses 2732408 [phylum] Pisuviricota 2732506 [class] Pisoniviricetes 76804 [order] Nidovirales 11118 [family] Coronaviridae 694002 [genus] Betacoronavirus 694009 [species] Severe acute re…
# Dealing with UnclassifiedTaxon as missing value
julia> taxa = [287, 157472, 9593, 2053489] .|> Taxon
# By deafult, UnclassifiedTaxon are stored
julia> taxa .|> Lineage .|> (x -> reformat(x, seven_rank)) .|> namedtuple |> DataFrame
4×7 DataFrame
Row │ superkingdom phylum class order family genus species
│ Taxon Taxon Abstract… Abstract… Abstract… Abstract… Taxon
─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2 [superkingdom] Bacteria 1224 [phylum] Proteobacteria 1236 [class] Gammaproteobacteria 72274 [order] Pseudomonadales 135621 [family] Pseudomonadaceae 286 [genus] Pseudomonas 287 [species] Pseudomonas aerugi…
2 │ 2 [superkingdom] Bacteria 1239 [phylum] Firmicutes 91061 [class] Bacilli 1385 [order] Bacillales Unclassified [family] unclassifi… Unclassified [genus] unclassifie… 157472 [species] uncultured Baci…
3 │ 2759 [superkingdom] Eukaryota 7711 [phylum] Chordata 40674 [class] Mammalia 9443 [order] Primates 9604 [family] Hominidae 9592 [genus] Gorilla 9593 [species] Gorilla gorilla
4 │ 2157 [superkingdom] Archaea 1655434 [phylum] Candidatus Loki… Unclassified [class] unclassifie… Unclassified [order] unclassifie… Unclassified [family] unclassifi… Unclassified [genus] unclassifie… 2053489 [species] Candidatus Lok…
# If set fill_by_missing to true in namedtuple, then missing are stored in DataFrame
julia> taxa .|> Lineage .|> (x -> reformat(x, seven_rank)) .|> (x -> namedtuple(x; fill_by_missing=true)) |> DataFrame
4×7 DataFrame
Row │ superkingdom phylum class order family genus species
│ Taxon Taxon Taxon? Taxon? Taxon? Taxon? Taxon
─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2 [superkingdom] Bacteria 1224 [phylum] Proteobacteria 1236 [class] Gammaproteobacteria 72274 [order] Pseudomonadales 135621 [family] Pseudomonadaceae 286 [genus] Pseudomonas 287 [species] Pseudomonas aerugi…
2 │ 2 [superkingdom] Bacteria 1239 [phylum] Firmicutes 91061 [class] Bacilli 1385 [order] Bacillales missing missing 157472 [species] uncultured Baci…
3 │ 2759 [superkingdom] Eukaryota 7711 [phylum] Chordata 40674 [class] Mammalia 9443 [order] Primates 9604 [family] Hominidae 9592 [genus] Gorilla 9593 [species] Gorilla gorilla
4 │ 2157 [superkingdom] Archaea 1655434 [phylum] Candidatus Loki… missing missing missing missing 2053489 [species] Candidatus Lok…