Taxonomy.jl
Taxonomy.jl is a julia package to handle NCBI-formatted taxonomic databases.
Now, this package only supports scientific name.
Notes for v0.2
- Moved AbstractTrees.jl v0.3 -> AbstractTrees.jl v0.4, following the breaking changes.
- Add API documents.
Installation
Install Taxonomy.jl as follows:
julia -e 'using Pkg; Pkg.add("Taxonomy")'
Usage
Download database
First, you need to download taxonomic data from NCBI's servers.
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xzvf taxdump.tar.gz
Create Taxonomy.DB object
You can create Taxonomy.DB object to store the data.
# Load the package
julia> using Taxonomy
julia> db = Taxonomy.DB("db/nodes.dmp","db/names.dmp") # Create a Taxonomy.DB objext from the path to each file
julia> db = Taxonomy.DB("/your/path/to/db","nodes.dmp","names.dmp") # Alternatively, create the object from the path to the directory and the name of each files
Taxon
You can construct a Taxon object from its taxonomic identifier and the Taxonomy.DB object.
julia> human = Taxon(9606, db) # species Homo sapiens
9606 [species] Homo sapiens
julia> gorilla = Taxon(9593, db) # species Gorilla gorilla
9593 [species] Gorilla gorilla
julia> bacillus = Taxon(1386,db) # genus Bacillus
1386 [genus] Bacillus
Each Taxon object has 4-field taxid, name, rank and db.
julia> @show human
human = 9606 [species] Homo sapiens
julia> @show human.taxid
human.taxid = 9606
julia> @show human.name
human.name = "Homo sapiens"
julia> @show human.rank
human.rank = :species
julia> @show human.db
human.db = Taxonomy.DB("db/nodes.dmp","db/names.dmp")
You can get a variety of information, such as rank, parent and children by using functions.
julia> rank(gorilla)
:species
julia> parent(gorilla)
9592 [genus] Gorilla
julia> children(bacillus)
249-element Array{Taxon,1}:
427072 [species] Bacillus chagannorensis
904295 [species] Bacillus ginsengisoli
1522318 [species] Bacillus kwashiorkori
1245522 [species] Bacillus thermophilus
1178786 [species] Bacillus thaonhiensis
1805474 [species] Bacillus mediterraneensis
⋮
324768 [species] Bacillus idriensis
745819 [species] Bacillus alkalicola
170350 [species] Bacillus deramificans
1522308 [species] Bacillus niameyensis
324767 [species] Bacillus infantis
Also, you can get the lowest common ancestor (LCA) of taxa.
julia> lca(human, gorilla)
207598 [subfamily] Homininae
julia> lca(human, gorilla, bacillus) # You can input as many as you want.
131567 [no rank] cellular organisms
julia> lca([human, gorilla, bacillus]) # Vector of taxon is also ok.
131567 [no rank] cellular organisms
Fuctions from AbstractTrees.jl can also be used.
julia> homininae = lca(human, gorilla)
julia> print_tree(homininae)
207598 [subfamily] Homininae
├─ 9596 [genus] Pan
│ ├─ 9597 [species] Pan paniscus
│ └─ 9598 [species] Pan troglodytes
│ ├─ 37010 [subspecies] Pan troglodytes schweinfurthii
│ ├─ 37011 [subspecies] Pan troglodytes troglodytes
│ ├─ 1294088 [subspecies] Pan troglodytes verus x troglodytes
│ ├─ 91950 [subspecies] Pan troglodytes vellerosus
│ ├─ 756884 [subspecies] Pan troglodytes ellioti
│ └─ 37012 [subspecies] Pan troglodytes verus
├─ 9605 [genus] Homo
│ ├─ 9606 [species] Homo sapiens
│ │ ├─ 63221 [subspecies] Homo sapiens neanderthalensis
│ │ └─ 741158 [subspecies] Homo sapiens subsp. 'Denisova'
│ ├─ 1425170 [species] Homo heidelbergensis
│ └─ 2665952 [no rank] environmental samples
│ └─ 2665953 [species] Homo sapiens environmental sample
└─ 9592 [genus] Gorilla
├─ 499232 [species] Gorilla beringei
│ ├─ 1159185 [subspecies] Gorilla beringei beringei
│ └─ 46359 [subspecies] Gorilla beringei graueri
└─ 9593 [species] Gorilla gorilla
├─ 183511 [subspecies] Gorilla gorilla uellensis
├─ 406788 [subspecies] Gorilla gorilla diehli
└─ 9595 [subspecies] Gorilla gorilla gorilla
Lineage
Lineage information can be acquired by using Lineage().
julia> lineage = Lineage(gorilla)
32-element Lineage:
1 [no rank] root
131567 [no rank] cellular organisms
2759 [superkingdom] Eukaryota
33154 [clade] Opisthokonta
33208 [kingdom] Metazoa
6072 [clade] Eumetazoa
33213 [clade] Bilateria
⋮
314293 [infraorder] Simiiformes
9526 [parvorder] Catarrhini
314295 [superfamily] Hominoidea
9604 [family] Hominidae
207598 [subfamily] Homininae
9592 [genus] Gorilla
9593 [species] Gorilla gorilla
Struct Lineage stores linage informaction in Vector-like format.
julia> lineage[1]
1 [no rank] root
julia> lineage[9]
7711 [phylum] Chordata
julia> lineage[end]
9593 [species] Gorilla gorilla
You can also access a Taxon in the Lineage using Symbol, such as :superkingdom, :family, :genus, :species and etc.(Only Symbols in CanonicalRank can be used).
julia> CanonicalRank
10-element Array{Symbol,1}:
:superkingdom
:kingdom
:phylum
:class
:order
:family
:genus
:species
:subspecies
:strain
julia> lineage[:order]
9443 [order] Primates
julia> lineage[:genus]
9592 [genus] Gorilla
You can use Between, From, Until, Cols and All selectors in more complex rank selection scenarios.
julia> lineage[Between(:order,:genus)]
8-element Lineage:
9443 [order] Primates
376913 [suborder] Haplorrhini
314293 [infraorder] Simiiformes
9526 [parvorder] Catarrhini
314295 [superfamily] Hominoidea
9604 [family] Hominidae
207598 [subfamily] Homininae
9592 [genus] Gorilla
julia> lineage[From(:family)]
4-element Lineage:
9604 [family] Hominidae
207598 [subfamily] Homininae
9592 [genus] Gorilla
9593 [species] Gorilla gorilla
julia> lineage[Until(:class)]
19-element Lineage:
1 [no rank] root
131567 [no rank] cellular organisms
2759 [superkingdom] Eukaryota
33154 [clade] Opisthokonta
33208 [kingdom] Metazoa
6072 [clade] Eumetazoa
33213 [clade] Bilateria
⋮
117570 [clade] Teleostomi
117571 [clade] Euteleostomi
8287 [superclass] Sarcopterygii
1338369 [clade] Dipnotetrapodomorpha
32523 [clade] Tetrapoda
32524 [clade] Amniota
40674 [class] Mammalia
Reformation of the lineage to your ranks can be performed by using reformat().
julia> myrank = [:superkingdom, :phylum, :class, :order, :family, :genus, :species]
julia> reformat(lineage, myrank)
7-element Lineage:
2759 [superkingdom] Eukaryota
7711 [phylum] Chordata
40674 [class] Mammalia
9443 [order] Primates
9604 [family] Hominidae
9592 [genus] Gorilla
9593 [species] Gorilla gorilla
If there is no corresponding taxon in the lineage to your ranks, then UnclassifiedTaxon will be stored.
julia> uncultured_bacillales = Taxon(157472,db)
57472 [species] uncultured Bacillales bacterium
julia> reformated = reformat(Lineage(uncultured_bacillales), myrank)
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 bacterium