Usage and Examples
Table of Contents
- Usage and Examples
- Before use
- taxonkit
- list
- lineage
- reformat
- name2taxid
- filter
- lca
- taxid-changelog
- genautocomplete
Before use
- Download and decompress
taxdump.tar.gz: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz - Copy
names.dmp,nodes.dmp,delnodes.dmpandmerged.dmpto data directory:$HOME/.taxonkit, e.g.,/home/shenwei/.taxonkit, - Optionally copy to some other directories, and later you can refer to using flag
--data-dir, or environment variableTAXONKIT_DB.
All-in-one command:
wget -c ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -zxvf taxdump.tar.gz
mkdir -p $HOME/.taxonkit
cp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit
taxonkit
TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit
Version: 0.7.2
Author: Wei Shen <shenwei356@gmail.com>
Source code: https://github.com/shenwei356/taxonkit
Documents : https://bioinf.shenwei.me/taxonkit
Citation : https://www.biorxiv.org/content/early/2019/01/08/513523
Dataset:
Please download and decompress "taxdump.tar.gz":
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
and copy "names.dmp", "nodes.dmp", "delnodes.dmp" and "merged.dmp" to data directory:
"/home/shenwei/.taxonkit"
or some other directory, and later you can refer to using flag --data-dir,
or environment variable TAXONKIT_DB
Usage:
taxonkit [command]
Available Commands:
filter Filter taxIDs by taxonomic rank range
genautocomplete generate shell autocompletion script
help Help about any command
lca Compute lowest common ancestor (LCA) for taxIDs
lineage Query taxonomic lineage of given taxIDs
list List taxonomic subtrees of given taxIDs
name2taxid Convert scientific names to taxIDs
reformat Reformat lineage in canonical ranks
taxid-changelog Create taxID changelog from dump archives
version print version information and check for update
Flags:
--data-dir string directory containing nodes.dmp and names.dmp (default "/home/shenwei/.taxonkit")
-h, --help help for taxonkit
--line-buffered use line buffering on output, i.e., immediately writing to stdin/file for every line of output
-o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-")
-j, --threads int number of CPUs. 4 is enough (default 4)
--verbose print verbose information
list
Usage
List taxonomic subtrees of given taxIDs
Examples:
$ taxonkit list --ids 9606 -n -r --indent " "
9606 [species] Homo sapiens
63221 [subspecies] Homo sapiens neanderthalensis
741158 [subspecies] Homo sapiens subsp. 'Denisova'
$ taxonkit list --ids 9606 --indent ""
9606
63221
741158
Usage:
taxonkit list [flags]
Flags:
-h, --help help for list
-i, --ids string taxID(s), multiple values should be separated by comma
-I, --indent string indent (default " ")
-J, --json output in JSON format. you can save the result in file with suffix ".json" and open with modern text editor
-n, --show-name output scientific name
-r, --show-rank output rank
Examples
-
Default usage.
$ taxonkit list --ids 9605,239934 9605 9606 63221 741158 1425170 2665952 2665953 239934 239935 349741 512293 512294 1131822 1262691 1263034 1679444 2608915 1131336 ... -
Removing indent. The list could be used to extract sequences from BLAST database with
blastdbcmd(see tutorial)$ taxonkit list --ids 9605,239934 --indent "" 9605 9606 63221 741158 1425170 2665952 2665953 239934 239935 349741 512293 512294 1131822 1262691 1263034 1679444 ...Performance: Time and memory usage for whole taxon tree:
$ # emptying the buffers cache $ su -c "free && sync && echo 3 > /proc/sys/vm/drop_caches && free" $ memusg -t taxonkit list --ids 1 --indent "" --verbose > t0.txt 21:05:01.782 [INFO] parsing merged file: /home/shenwei/.taxonkit/names.dmp 21:05:01.782 [INFO] parsing names file: /home/shenwei/.taxonkit/names.dmp 21:05:01.782 [INFO] parsing delnodes file: /home/shenwei/.taxonkit/names.dmp 21:05:01.816 [INFO] 61023 merged nodes parsed 21:05:01.889 [INFO] 437929 delnodes parsed 21:05:03.178 [INFO] 2303979 names parsed elapsed time: 3.290s peak rss: 742.77 MB -
Adding names
$ taxonkit list --show-rank --show-name --indent " " --ids 9605,239934 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 239934 [genus] Akkermansia 239935 [species] Akkermansia muciniphila 349741 [strain] Akkermansia muciniphila ATCC BAA-835 512293 [no rank] environmental samples 512294 [species] uncultured Akkermansia sp. 1131822 [species] uncultured Akkermansia sp. SMG25 1262691 [species] Akkermansia sp. CAG:344 1263034 [species] Akkermansia muciniphila CAG:154 1679444 [species] Akkermansia glycaniphila 2608915 [no rank] unclassified Akkermansia 1131336 [species] Akkermansia sp. KLE1605 1574264 [species] Akkermansia sp. KLE1797 ...Performance: Time and memory usage for whole taxonomy tree:
$ # emptying the buffers cache $ su -c "free && sync && echo 3 > /proc/sys/vm/drop_caches && free" $ memusg -t taxonkit list --show-rank --show-name --ids 1 > t1.txt elapsed time: 5.341s peak rss: 1.04 GB -
Output in JSON format, you can easily collapse and uncollapse taxonomy tree in modern text editor.
$ taxonkit list --show-rank --show-name --indent " " --ids 9605,239934 --json { "9605 [genus] Homo": { "9606 [species] Homo sapiens": { "63221 [subspecies] Homo sapiens neanderthalensis": { }, "741158 [subspecies] Homo sapiens subsp. 'Denisova'": { } }, "1425170 [species] Homo heidelbergensis": { } }, "239934 [genus] Akkermansia": { "239935 [species] Akkermansia muciniphila": { "349741 [no rank] Akkermansia muciniphila ATCC BAA-835": { } }, "512293 [no rank] environmental samples": { "512294 [species] uncultured Akkermansia sp.": { }, "1131822 [species] uncultured Akkermansia sp. SMG25": { }, "1262691 [species] Akkermansia sp. CAG:344": { }, "1263034 [species] Akkermansia muciniphila CAG:154": { } }, "1679444 [species] Akkermansia glycaniphila": { }, "2608915 [no rank] unclassified Akkermansia": { "1131336 [species] Akkermansia sp. KLE1605": { }, "1574264 [species] Akkermansia sp. KLE1797": { }, "1574265 [species] Akkermansia sp. KLE1798": { }, "1638783 [species] Akkermansia sp. UNK.MGS-1": { }, "1755639 [species] Akkermansia sp. MC_55": { } } } }Snapshot of taxonomy (taxid 1) in kate:
lineage
Usage
Query taxonomic lineage of given taxIDs
Input:
- List of taxIDs, one taxID per line.
- Or tab-delimited format, please specify taxID field
with flag -i/--taxid-field (default 1).
- Supporting (gzipped) file or STDIN.
Output:
1. Input line data.
2. (Optional) Status code (-c/--show-status-code), values:
- "-1" for queries not found in whole database.
- "0" for deleted taxIDs, provided by "delnodes.dmp".
- New taxIDs for merged taxIDs, provided by "merged.dmp".
- Taxids for these found in "nodes.dmp".
3. Lineage, delimiter can be changed with flag -d/--delimiter.
4. (Optional) Lineage in taxIDs (-t/--show-lineage-taxids)
5. (Optional) Rank (-r/--show-rank)
Filter out invalid and deleted taxids, and replace merged
taxids with new ones:
# input is one-column-taxid
$ taxonkit lineage -c taxids.txt \
| awk '$2>0' \
| cut -f 2-
# taxids are in 3rd field in a 4-columns tab-delimited file,
# for $5, where 5 = 4 + 1.
$ cat input.txt \
| taxonkit lineage -c -i 3 \
| csvtk filter2 -H -t -f '$5>0' \
| csvtk -H -t cut -f -3
Usage:
taxonkit lineage [flags]
Flags:
-d, --delimiter string field delimiter in lineage (default ";")
-h, --help help for lineage
-L, --no-lineage do not show lineage, when user just want names or/and ranks
-R, --show-lineage-ranks appending ranks of all levels
-t, --show-lineage-taxids appending lineage consisting of taxids
-n, --show-name appending scientific name
-r, --show-rank appending rank of taxids
-c, --show-status-code show status code before lineage
-i, --taxid-field int field index of taxid. input data should be tab-separated (default 1)
Examples
-
Full lineage:
# note that 123124124 is a fake taxid, 3 was deleted, 92489,1458427 were merged $ cat taxids.txt 9606 9913 376619 349741 239935 314101 11932 1327037 123124124 3 92489 1458427 $ taxonkit lineage taxids.txt | tee lineage.txt 19:22:13.077 [WARN] taxid 92489 was merged into 796334 19:22:13.077 [WARN] taxid 1458427 was merged into 1458425 19:22:13.077 [WARN] taxid 123124124 not found 19:22:13.077 [WARN] taxid 3 was deleted 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 9913 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bos taurus 376619 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis;Francisella tularensis subsp. holarctica;Francisella tularensis subsp. holarctica LVS 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B 11932 Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle 1327037 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y 123124124 3 92489 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae 1458427 cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raicheisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei -
Speed.
$ time echo 9606 | taxonkit lineage 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens real 0m1.190s user 0m2.365s sys 0m0.170s # all taxIDs $ time taxonkit list --ids 1 --indent "" | taxonkit lineage > t real 0m4.249s user 0m16.418s sys 0m1.221s -
Checking deleted or merged taxids
$ taxonkit lineage --show-status-code taxids.txt | tee lineage.withcode.txt # valid $ cat lineage.withcode.txt | awk '$2 > 0' | cut -f 1,2 9606 9606 9913 9913 376619 376619 349741 349741 239935 239935 314101 314101 11932 11932 1327037 1327037 92489 796334 1458427 1458425 # merged $ cat lineage.withcode.txt | awk '$2 > 0 && $2 != $1' | cut -f 1,2 92489 796334 1458427 1458425 # deleted $ cat lineage.withcode.txt | awk '$2 == 0' | cut -f 1 3 # invalid $ cat lineage.withcode.txt | awk '$2 < 0' | cut -f 1 123124124 -
Filter out invalid and deleted taxids, and replace merged taxids with new ones, you may install csvtk.
# input is one-column-taxid $ taxonkit lineage -c taxids.txt \ | awk '$2>0' \ | cut -f 2- # taxids are in 3rd field in a 4-columns tab-delimited file, # for $5, where 5 = 4 + 1. $ cat input.txt \ | taxonkit lineage -c -i 3 \ | csvtk filter2 -H -t -f '$5>0' \ | csvtk -H -t cut -f -3 -
Only show name and rank.
$ taxonkit lineage -r -n -L taxids.txt \ | csvtk pretty -t 9606 Homo sapiens species 9913 Bos taurus species 376619 Francisella tularensis subsp. holarctica LVS strain 349741 Akkermansia muciniphila ATCC BAA-835 strain 239935 Akkermansia muciniphila species 314101 uncultured murine large bowel bacterium BAC 54B species 11932 Mouse Intracisternal A-particle species 1327037 Croceibacter phage P2559Y species 123124124 3 92489 Erwinia oleae species 1458427 Serpentinomonas raichei species -
Show lineage consisting of taxids:
$ taxonkit lineage -t taxids.txt 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;9606 9913 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bos taurus 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314145;91561;9845;35500;9895;27592;9903;9913 376619 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis;Francisella tularensis subsp. holarctica;Francisella tularensis subsp. holarctica LVS 131567;2;1224;1236;72273;34064;262;263;119857;376619 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B 131567;2;48479;314101 11932 Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle 10239;2559587;2732397;2732409;2732514;2169561;11632;35276;11749;11932 1327037 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y 10239;2731341;2731360;2731618;2731619;28883;10699;196894;1327037 123124124 3 92489 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae 131567;2;1224;1236;91347;1903409;551;796334 1458427 cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei 131567;2;1224;28216;80840;80864;2490452;1458425or read taxids from STDIN:
$ cat taxids.txt | taxonkit lineage -
And ranks of all nodes:
$ echo 2697049 \ | taxonkit lineage -t -R \ | csvtk transpose -Ht 2697049 Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049 superkingdom;clade;kingdom;phylum;class;order;suborder;family;subfamily;genus;subgenus;species;no rankAnother way to show lineage detail of a taxID
$ echo 2697049 \ | taxonkit lineage -t \ | csvtk cut -Ht -f 3 \ | csvtk unfold -Ht -f 1 -s ";" \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk pretty -t 10239 superkingdom Viruses 2559587 clade Riboviria 2732396 kingdom Orthornavirae 2732408 phylum Pisuviricota 2732506 class Pisoniviricetes 76804 order Nidovirales 2499399 suborder Cornidovirineae 11118 family Coronaviridae 2501931 subfamily Orthocoronavirinae 694002 genus Betacoronavirus 2509511 subgenus Sarbecovirus 694009 species Severe acute respiratory syndrome-related coronavirus 2697049 no rank Severe acute respiratory syndrome coronavirus 2
reformat
Usage
Reformat lineage in canonical ranks
Output format can be formated by flag --format, available placeholders:
{k}: superkingdom
{p}: phylum
{c}: class
{o}: order
{f}: family
{g}: genus
{s}: species
{t}: subspecies/strain
{S}: subspecies
{T}: strain
When these's no nodes of rank "subspecies" nor "stain",
you can switch -S/--pseudo-strain to use the node with lowest rank
as subspecies/strain name, if which rank is lower than "species".
This flag affects {t}, {S}, {T}.
Output format can contains some escape charactors like "\t".
This command appends reformated lineage to the input line.
The corresponding taxIDs of reformated lineage can be provided as another
column by flag "-t/--show-lineage-taxids".
Usage:
taxonkit reformat [flags]
Flags:
-P, --add-prefix add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X
-d, --delimiter string field delimiter in input lineage (default ";")
-F, --fill-miss-rank fill missing rank with lineage information of the next higher rank
-f, --format string output format, placeholders of rank are needed (default "{k};{p};{c};{o};{f};{g};{s}")
-h, --help help for reformat
-i, --lineage-field int field index of lineage. data should be tab-separated (default 2)
-r, --miss-rank-repl string replacement string for missing rank
-p, --miss-rank-repl-prefix string prefix for estimated taxon level (default "unclassified ")
-R, --miss-taxid-repl string replacement string for missing taxid
--prefix-S string prefix for subspecies, used along with flag -P/--add-prefix (default "S__")
--prefix-T string prefix for strain, used along with flag -P/--add-prefix (default "T__")
--prefix-c string prefix for class, used along with flag -P/--add-prefix (default "c__")
--prefix-f string prefix for family, used along with flag -P/--add-prefix (default "f__")
--prefix-g string prefix for genus, used along with flag -P/--add-prefix (default "g__")
--prefix-k string prefix for superkingdom, used along with flag -P/--add-prefix (default "k__")
--prefix-o string prefix for order, used along with flag -P/--add-prefix (default "o__")
--prefix-p string prefix for phylum, used along with flag -P/--add-prefix (default "p__")
--prefix-s string prefix for species, used along with flag -P/--add-prefix (default "s__")
--prefix-t string prefix for subspecies/strain, used along with flag -P/--add-prefix (default "t__")
-S, --pseudo-strain use the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain". This flag affects {t}, {S}, {T}
-t, --show-lineage-taxids show corresponding taxids of reformated lineage
-T, --trim do not fill missing rank lower than current rank
Examples:
-
Example lineage (produced by:
taxonkit lineage taxids.txt | awk '$2!=""' > lineage.txt).$ cat lineage.txt 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 9913 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bos taurus 376619 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis;Francisella tularensis subsp. holarctica;Francisella tularensis subsp. holarctica LVS 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B 11932 Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle 1327037 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y 92489 cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae 1458427 cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei -
Default output format (
"{k};{p};{c};{o};{f};{g};{s}").# reformated lineages are appended to the input data $ taxonkit reformat lineage.txt ... 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila ... $ $ taxonkit reformat lineage.txt | tee lineage.txt.reformat $ cut -f 1,3 lineage.txt.reformat 9606 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens 9913 Eukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;Bos taurus 376619 Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis 349741 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 239935 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 314101 Bacteria;;;;;;uncultured murine large bowel bacterium BAC 54B 11932 Viruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle 1327037 Viruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;;Croceibacter phage P2559Y 92489 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae 1458427 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei # aligned $ cat lineage.txt \ | taxonkit reformat \ | csvtk -H -t cut -f 1,3 \ | csvtk -H -t sep -f 2 -s ';' -R \ | csvtk add-header -t -n taxid,kindom,phylum,class,order,family,genus,species \ | csvtk pretty -t taxid kindom phylum class order family genus species 9606 Eukaryota Chordata Mammalia Primates Hominidae Homo Homo sapiens 9913 Eukaryota Chordata Mammalia Artiodactyla Bovidae Bos Bos taurus 376619 Bacteria Proteobacteria Gammaproteobacteria Thiotrichales Francisellaceae Francisella Francisella tularensis 349741 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia Akkermansia muciniphila 239935 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia Akkermansia muciniphila 314101 Bacteria uncultured murine large bowel bacterium BAC 54B 11932 Viruses Artverviricota Revtraviricetes Ortervirales Retroviridae Intracisternal A-particles Mouse Intracisternal A-particle 1327037 Viruses Uroviricota Caudoviricetes Caudovirales Siphoviridae Croceibacter phage P2559Y 92489 Bacteria Proteobacteria Gammaproteobacteria Enterobacterales Erwiniaceae Erwinia Erwinia oleae 1458427 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Serpentinomonas Serpentinomonas raichei -
And
subspecies/stain({t}),subspecies({S}), andstrain({T}) are also available.# default operation $ echo -ne "239935\n83333\n1408252\n2697049\n2605619\n" \ | taxonkit lineage -n -r \ | taxonkit reformat -f '{t};{S};{T}' \ | csvtk -H -t cut -f 1,4,3,5 \ | csvtk -H -t sep -f 4 -s ';' -R \ | csvtk -H -t add-header -n "taxid,rank,name,subspecies/stain,subspecies,strain" \ | csvtk pretty -t taxid rank name subspecies/stain subspecies strain 239935 species Akkermansia muciniphila 83333 strain Escherichia coli K-12 Escherichia coli K-12 Escherichia coli K-12 1408252 subspecies Escherichia coli R178 Escherichia coli R178 Escherichia coli R178 2697049 no rank Severe acute respiratory syndrome coronavirus 2 2605619 no rank Escherichia coli O16:H48 # fill missing ranks # see example below for -F/--fill-miss-rank # $ echo -ne "239935\n83333\n1408252\n2697049\n2605619\n" \ | taxonkit lineage -n -r \ | taxonkit reformat -f '{t};{S};{T}' --fill-miss-rank \ | csvtk -H -t cut -f 1,4,3,5 \ | csvtk -H -t sep -f 4 -s ';' -R \ | csvtk -H -t add-header -n "taxid,rank,name,subspecies/stain,subspecies,strain" \ | csvtk pretty -t taxid rank name subspecies/stain subspecies strain 239935 species Akkermansia muciniphila unclassified Akkermansia muciniphila subspecies/strain unclassified Akkermansia muciniphila subspecies unclassified Akkermansia muciniphila strain 83333 strain Escherichia coli K-12 Escherichia coli K-12 unclassified Escherichia coli subspecies Escherichia coli K-12 1408252 subspecies Escherichia coli R178 Escherichia coli R178 Escherichia coli R178 unclassified Escherichia coli R178 strain 2697049 no rank Severe acute respiratory syndrome coronavirus 2 unclassified Severe acute respiratory syndrome-related coronavirus subspecies/strain unclassified Severe acute respiratory syndrome-related coronavirus subspecies unclassified Severe acute respiratory syndrome-related coronavirus strain 2605619 no rank Escherichia coli O16:H48 unclassified Escherichia coli subspecies/strain unclassified Escherichia coli subspecies unclassified Escherichia coli strain # When these's no nodes of rank "subspecies" nor "stain", # you can switch -S/--pseudo-strain to use the node with lowest rank # as subspecies/strain name, if which rank is lower than "species" # $ echo -ne "239935\n83333\n1408252\n2697049\n2605619\n" \ | taxonkit lineage -n -r \ | taxonkit reformat -f '{t};{S};{T}' --fill-miss-rank --pseudo-strain \ | csvtk -H -t cut -f 1,4,3,5 \ | csvtk -H -t sep -f 4 -s ';' -R \ | csvtk -H -t add-header -n "taxid,rank,name,subspecies/stain,subspecies,strain" \ | csvtk pretty -t taxid rank name subspecies/stain subspecies strain 239935 species Akkermansia muciniphila unclassified Akkermansia muciniphila subspecies/strain unclassified Akkermansia muciniphila subspecies unclassified Akkermansia muciniphila strain 83333 strain Escherichia coli K-12 Escherichia coli K-12 unclassified Escherichia coli subspecies Escherichia coli K-12 1408252 subspecies Escherichia coli R178 Escherichia coli R178 Escherichia coli R178 unclassified Escherichia coli R178 strain 2697049 no rank Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 2605619 no rank Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 -
Add prefix (
-P/--add-prefix).$ cat lineage.txt \ | taxonkit reformat -P \ | csvtk -H -t cut -f 1,3 9606 k__Eukaryota;p__Chordata;c__Mammalia;o__Primates;f__Hominidae;g__Homo;s__Homo sapiens 9913 k__Eukaryota;p__Chordata;c__Mammalia;o__Artiodactyla;f__Bovidae;g__Bos;s__Bos taurus 376619 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Francisellaceae;g__Francisella;s__Francisella tularensis 349741 k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia muciniphila 239935 k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia muciniphila 314101 k__Bacteria;p__;c__;o__;f__;g__;s__uncultured murine large bowel bacterium BAC 54B 11932 k__Viruses;p__Artverviricota;c__Revtraviricetes;o__Ortervirales;f__Retroviridae;g__Intracisternal A-particles;s__Mouse Intracisternal A-particle 1327037 k__Viruses;p__Uroviricota;c__Caudoviricetes;o__Caudovirales;f__Siphoviridae;g__;s__Croceibacter phage P2559Y 92489 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Erwiniaceae;g__Erwinia;s__Erwinia oleae 1458427 k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Serpentinomonas;s__Serpentinomonas raichei -
Show corresponding taxids of reformated lineage (flag
-t/--show-lineage-taxids)$ cat lineage.txt \ | taxonkit reformat -t \ | csvtk -H -t cut -f 1,4 \ | csvtk -H -t sep -f 2 -s ';' -R \ | csvtk add-header -t -n taxid,kindom,phylum,class,order,family,genus,species \ | csvtk pretty -t taxid kindom phylum class order family genus species 9606 2759 7711 40674 9443 9604 9605 9606 9913 2759 7711 40674 91561 9895 9903 9913 376619 2 1224 1236 72273 34064 262 263 349741 2 74201 203494 48461 1647988 239934 239935 239935 2 74201 203494 48461 1647988 239934 239935 314101 2 314101 11932 10239 2732409 2732514 2169561 11632 11749 11932 1327037 10239 2731618 2731619 28883 10699 1327037 92489 2 1224 1236 91347 1903409 551 796334 1458427 2 1224 28216 80840 80864 2490452 1458425 -
Use custom symbols for unclassfied ranks (
-r/--miss-rank-repl)$ taxonkit reformat lineage.txt -r "__" | cut -f 3 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens Eukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;Bos taurus Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;__;__;__;__;__;uncultured murine large bowel bacterium BAC 54B Viruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Viruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;__;Croceibacter phage P2559Y Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei $ taxonkit reformat lineage.txt -r Unassigned | cut -f 3 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens Eukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;Bos taurus Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisella tularensis Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Unassigned;Unassigned;Unassigned;Unassigned;Unassigned;uncultured murine large bowel bacterium BAC 54B Viruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Viruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Unassigned;Croceibacter phage P2559Y Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei -
Estimate and fill missing rank with original lineage information (
-F, --fill-miss-rank, very useful for formatting input data for LEfSe). You can change the prefix "unclassified" using flag-p/--miss-rank-repl-prefix.$ cat lineage.txt \ | taxonkit reformat -F \ | csvtk -H -t cut -f 1,3 \ | csvtk -H -t sep -f 2 -s ';' -R \ | csvtk add-header -t -n taxid,kindom,phylum,class,order,family,genus,species \ | csvtk pretty -t taxid kindom phylum class order family genus species 9606 Eukaryota Chordata Mammalia Primates Hominidae Homo Homo sapiens 9913 Eukaryota Chordata Mammalia Artiodactyla Bovidae Bos Bos taurus 376619 Bacteria Proteobacteria Gammaproteobacteria Thiotrichales Francisellaceae Francisella Francisella tularensis 349741 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia Akkermansia muciniphila 239935 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia Akkermansia muciniphila 314101 Bacteria unclassified Bacteria phylum unclassified Bacteria class unclassified Bacteria order unclassified Bacteria family unclassified Bacteria genus uncultured murine large bowel bacterium BAC 54B 11932 Viruses Artverviricota Revtraviricetes Ortervirales Retroviridae Intracisternal A-particles Mouse Intracisternal A-particle 1327037 Viruses Uroviricota Caudoviricetes Caudovirales Siphoviridae unclassified Siphoviridae genus Croceibacter phage P2559Y 92489 Bacteria Proteobacteria Gammaproteobacteria Enterobacterales Erwiniaceae Erwinia Erwinia oleae 1458427 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Serpentinomonas Serpentinomonas raichei -
Only some ranks.
$ cat lineage.txt \ | taxonkit reformat -F -f "{s};{p}"\ | csvtk -H -t cut -f 1,3 \ | csvtk -H -t sep -f 2 -s ';' -R \ | csvtk add-header -t -n taxid,species,phylum \ | csvtk pretty -t taxid species phylum 9606 Homo sapiens Chordata 9913 Bos taurus Chordata 376619 Francisella tularensis Proteobacteria 349741 Akkermansia muciniphila Verrucomicrobia 239935 Akkermansia muciniphila Verrucomicrobia 314101 uncultured murine large bowel bacterium BAC 54B unclassified Bacteria phylum 11932 Mouse Intracisternal A-particle Artverviricota 1327037 Croceibacter phage P2559Y Uroviricota 92489 Erwinia oleae Proteobacteria 1458427 Serpentinomonas raichei Proteobacteria -
For some taxids which rank is higher than the lowest rank in
-f/--format, use-T/--trimto avoid fill missing rank lower than current rank.$ echo -ne "2\n239934\n239935\n" \ | taxonkit lineage \ | taxonkit reformat -T \ | sed -r "s/;+$//" \ | csvtk -H -t cut -f 1,3 2 Bacteria 239934 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia 239935 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila -
Support tab in format string
$ echo 9606 \ | taxonkit lineage \ | taxonkit reformat -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}\t{S}" \ | csvtk cut -t -f -2 9606 Eukaryota Chordata Mammalia Primates Hominidae Homo Homo sapiens -
List seven-level lineage for all taxIDs.
# replace empty taxon with "Unassigned" $ taxonkit list --ids 1 \ | taxonkit lineage \ | taxonkit reformat -r Unassigned | gzip -c > all.lineage.tsv.gz # tab-delimited seven-levels $ taxonkit list --ids 1 \ | taxonkit lineage \ | taxonkit reformat -r Unassigned -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" \ | csvtk cut -H -t -f -2 \ | head -n 5 \ | csvtk pretty -t # 8-level $ taxonkit list --ids 1 \ | taxonkit lineage \ | taxonkit reformat -r Unassigned -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}\t{t}" \ | csvtk cut -H -t -f -2 \ | head -n 5 \ | csvtk pretty -t # Fill and trim $ memusg -t -s ' taxonkit list --ids 1 \ | taxonkit lineage \ | taxonkit reformat -F -T \ | sed -r "s/;+$//" \ | gzip -c > all.lineage.tsv.gz ' elapsed time: 19.930s peak rss: 6.25 GB -
From taxid to 7-ranks lineage:
$ cat taxids.txt | taxonkit lineage | taxonkit reformat
name2taxid
Usage
Convert scientific names to taxIDs
Attention:
1. Some taxIDs share the same scientific names, e.g, Drosophila.
These input lines are duplicated with multiple taxIDs.
$ echo Drosophila | taxonkit name2taxid | taxonkit lineage -i 2 -r -L
Drosophila 7215 genus
Drosophila 32281 subgenus
Drosophila 2081351 genus
Usage:
taxonkit name2taxid [flags]
Flags:
-h, --help help for name2taxid
-i, --name-field int field index of name. data should be tab-separated (default 1)
-s, --sci-name only searching scientific names
-r, --show-rank show rank
Examples
Example data
$ cat names.txt
Homo sapiens
Akkermansia muciniphila ATCC BAA-835
Akkermansia muciniphila
Mouse Intracisternal A-particle
Wei Shen
uncultured murine large bowel bacterium BAC 54B
Croceibacter phage P2559Y
-
Default.
# taxonkit name2taxid names.txt $ cat names.txt | taxonkit name2taxid | csvtk pretty -t Homo sapiens 9606 Akkermansia muciniphila ATCC BAA-835 349741 Akkermansia muciniphila 239935 Mouse Intracisternal A-particle 11932 Wei Shen uncultured murine large bowel bacterium BAC 54B 314101 Croceibacter phage P2559Y 1327037 -
Show rank.
$ cat names.txt | taxonkit name2taxid --show-rank | csvtk pretty -t Homo sapiens 9606 species Akkermansia muciniphila ATCC BAA-835 349741 strain Akkermansia muciniphila 239935 species Mouse Intracisternal A-particle 11932 species Wei Shen uncultured murine large bowel bacterium BAC 54B 314101 species Croceibacter phage P2559Y 1327037 species -
From name to lineage.
$ cat names.txt | taxonkit name2taxid | taxonkit lineage --taxid-field 2 Homo sapiens 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens Akkermansia muciniphila ATCC BAA-835 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 Akkermansia muciniphila 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Mouse Intracisternal A-particle 11932 Viruses;Ortervirales;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Wei Shen uncultured murine large bowel bacterium BAC 54B 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B Croceibacter phage P2559Y 1327037 Viruses;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y -
Some taxIDs share the same scientific names, e.g, Drosophila.
$ echo Drosophila \ | taxonkit name2taxid \ | taxonkit lineage -i 2 -r \ | taxonkit reformat -i 3 \ | csvtk cut -H -t -f 1,2,4,5 \ | csvtk pretty -t Drosophila 7215 genus Eukaryota;Arthropoda;Insecta;Diptera;Drosophilidae;Drosophila; Drosophila 32281 subgenus Eukaryota;Arthropoda;Insecta;Diptera;Drosophilidae;Drosophila; Drosophila 2081351 genus Eukaryota;Basidiomycota;Agaricomycetes;Agaricales;Psathyrellaceae;Drosophila;
filter
Usage
Filter taxIDs by taxonomic rank range
Attentions:
1. Flag -L/--lower-than and -H/--higher-than are exclusive, and can be
used along with -E/--equal-to which values can be different.
2. A list of pre-ordered ranks is in ~/.taxonkit/ranks.txt, you can use
your list by -r/--rank-file, the format specification is below.
3. All ranks in taxonomy database should be defined in rank file.
4. Ranks can be removed with black list via -B/--black-list.
5. TaxIDs with no rank can be optionally discarded by -N/--discard-noranks.
6. But when filtering with -L/--lower-than, you can use
-n/--save-predictable-norank to save some special ranks without order,
where rank of the closest higher node is still lower than rank cutoff.
Rank file:
1. Blank lines or lines starting with "#" are ignored.
2. Ranks are in decending order and case ignored.
3. Ranks with same order should be in one line separated with comma (",", no space).
4. Ranks without order should be assigned a prefix symbol "!" for each rank.
Usage:
taxonkit filter [flags]
Flags:
-B, --black-list strings black list of ranks to discard, e.g., '-B "no rank" -B "clade"
-N, --discard-noranks discard all ranks without order, type "taxonkit filter --help" for details
-R, --discard-root discard root taxid, defined by --root-taxid
-E, --equal-to strings output taxIDs with rank equal to some ranks, multiple values can be separated with comma "," (e.g., -E "genus,species"), or give multiple times (e.g., -E genus -E species)
-h, --help help for filter
-H, --higher-than string output taxIDs with rank higher than a rank, exclusive with --lower-than
--list-order list user defined ranks in order, from "$HOME/.taxonkit/ranks.txt"
--list-ranks list ordered ranks in taxonomy database, sorted in user defined order
-L, --lower-than string output taxIDs with rank lower than a rank, exclusive with --higher-than
-r, --rank-file string user-defined ordered taxonomic ranks, type "taxonkit filter --help" for details
--root-taxid uint32 root taxid (default 1)
-n, --save-predictable-norank do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff
-i, --taxid-field int field index of taxid. input data should be tab-separated (default 1)
Examples
-
Example data
$ echo 349741 | taxonkit lineage -t | cut -f 3 | sed 's/;/\n/g' > taxids2.txt $ cat taxids2.txt 131567 2 1783257 74201 203494 48461 1647988 239934 239935 349741 $ cat taxids2.txt | taxonkit lineage -r | csvtk -Ht cut -f 1,3,2 | csvtk pretty -t 131567 no rank cellular organisms 2 superkingdom cellular organisms;Bacteria 1783257 clade cellular organisms;Bacteria;PVC group 74201 phylum cellular organisms;Bacteria;PVC group;Verrucomicrobia 203494 class cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae 48461 order cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales 1647988 family cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae 239934 genus cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia 239935 species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 349741 strain cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 -
Equal to certain rank(s) (
-E/--equal-to)$ cat taxids2.txt \ | taxonkit filter -E Phylum -E Class \ | taxonkit lineage -r \ | csvtk -Ht cut -f 1,3,2 \ | csvtk pretty -t 74201 phylum cellular organisms;Bacteria;PVC group;Verrucomicrobia 203494 class cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae -
Lower than a rank (
-L/--lower-than)$ cat taxids2.txt \ | taxonkit filter -L genus \ | taxonkit lineage -r -n -L \ | csvtk -Ht cut -f 1,3,2 \ | csvtk pretty -t 239935 species Akkermansia muciniphila 349741 strain Akkermansia muciniphila ATCC BAA-835 -
Higher than a rank (
-H/--higher-than)$ cat taxids2.txt \ | taxonkit filter -H phylum \ | taxonkit lineage -r -n -L \ | csvtk -Ht cut -f 1,3,2 \ | csvtk pretty -t 2 superkingdom Bacteria -
"no rank" and "clade" have no rank and can be filter out via
-N/--discard-noranks. Futher ranks can be removed with black list via-B/--black-list# 562 is taxID of Escherichia coli $ taxonkit list --ids 562 \ | taxonkit filter -L species \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk freq -Ht -f 2 -nr \ | csvtk pretty -t strain 2950 no rank 149 serotype 141 serogroup 95 isolate 1 subspecies 1 $ taxonkit list --ids 562 \ | taxonkit filter -L species -N -B strain \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk freq -Ht -f 2 -nr \ | csvtk pretty -t serotype 141 serogroup 95 isolate 1 subspecies 1 -
Combine of
-L/-Hwith-E.$ cat taxids2.txt \ | taxonkit filter -L genus -E genus \ | taxonkit lineage -r -n -L \ | csvtk -Ht cut -f 1,3,2 \ | csvtk pretty -t 239934 genus Akkermansia 239935 species Akkermansia muciniphila 349741 strain Akkermansia muciniphila ATCC BAA-835 -
Special cases of "no rank". (
-n/--save-predictable-norank). When filtering with-L/--lower-than, you can use-n/--save-predictable-norankto save some special ranks without order, where rank of the closest higher node is still lower than rank cutoff.$ echo -ne "2605619\n1327037\n" \ | taxonkit lineage -t \ | csvtk cut -Ht -f 3 \ | csvtk unfold -Ht -f 1 -s ";" \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk pretty -t 131567 no rank cellular organisms 2 superkingdom Bacteria 1224 phylum Proteobacteria 1236 class Gammaproteobacteria 91347 order Enterobacterales 543 family Enterobacteriaceae 561 genus Escherichia 562 species Escherichia coli 2605619 no rank Escherichia coli O16:H48 10239 superkingdom Viruses 2731341 clade Duplodnaviria 2731360 clade Heunggongvirae 2731618 phylum Uroviricota 2731619 class Caudoviricetes 28883 order Caudovirales 10699 family Siphoviridae 196894 no rank unclassified Siphoviridae 1327037 species Croceibacter phage P2559Y # save taxids $ echo -ne "2605619\n1327037\n" \ | taxonkit lineage -t \ | csvtk cut -Ht -f 3 \ | csvtk unfold -Ht -f 1 -s ";" \ | tee taxids4.txt 131567 2 1224 1236 91347 543 561 562 2605619 10239 2731341 2731360 2731618 2731619 28883 10699 196894 1327037Now, filter nodes of rank <= species.
$ cat taxids4.txt \ | taxonkit filter -L species -E species -N -n \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk pretty -t 562 species Escherichia coli 2605619 no rank Escherichia coli O16:H48 1327037 species Croceibacter phage P2559YNote that 2605619 (no rank) is saved because its parent node 562 is <= species.
lca
Usage
Compute lowest common ancestor (LCA) for taxIDs
Attention:
1. This command computes LCA taxID for a list of taxIDs
in a field ("-i/--taxids-field) of tab-delimited file or STDIN.
2. TaxIDs should have the same separater ("-s/--separater"),
single charactor separater is prefered.
3. Empty lines or lines without valid taxIDs in the field are omitted.
4. If some taxIDs are not found in database, it returns 0.
Examples:
$ echo 239934, 239935, 349741 | taxonkit lca -s ", "
239934, 239935, 349741 239934
$ echo 239934 239935 349741 9606 | taxonkit lca
239934 239935 349741 9606 131567
Usage:
taxonkit lca [flags]
Flags:
-h, --help help for lca
-s, --separater string separater for taxIDs (default " ")
-D, --skip-deleted skip deleted taxIDs and compute with left ones
-U, --skip-unfound skip unfound taxIDs and compute with left ones
-i, --taxids-field int field index of taxid. input data should be tab-separated (default 1)
Examples:
-
Example data
$ taxonkit list --ids 9605 -nr --indent " " 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 -
Simple one
$ echo 63221 2665953 | taxonkit lca 63221 2665953 9605 -
Custom field (
-i/--taxids-field) and separater (-s/--separater).$ echo -ne "a\t63221,2665953\nb\t63221, 741158\n" a 63221,2665953 b 63221, 741158 $ echo -ne "a\t63221,2665953\nb\t63221, 741158\n" \ | taxonkit lca -i 2 -s "," a 63221,2665953 9605 b 63221, 741158 9606 -
Merged taxIDs.
# merged $ echo 92487 92488 92489 | taxonkit lca 10:08:26.578 [WARN] taxid 92489 was merged into 796334 92487 92488 92489 1236 -
Deleted taxIDs, you can ommit theses and continue compute with left onces with (
-D/--skip-deleted).$ echo 1 2 3 | taxonkit lca 10:30:17.678 [WARN] taxid 3 not found 1 2 3 0 $ time echo 1 2 3 | taxonkit lca -D 10:29:31.828 [WARN] taxid 3 was deleted 1 2 3 1 -
TaxIDs not found in database, you can ommit theses and continue compute with left onces with (
-U/--skip-unfound).$ echo 61021 61022 11111111 | taxonkit lca 10:31:44.929 [WARN] taxid 11111111 not found 61021 61022 11111111 0 $ echo 61021 61022 11111111 | taxonkit lca -U 10:32:02.772 [WARN] taxid 11111111 not found 61021 61022 11111111 2628496
taxid-changelog
Usage
Create taxID changelog from dump archives
Steps:
# dependencies:
# rush - https://github.com/shenwei356/rush/
mkdir -p archive; cd archive;
# --------- download ---------
# option 1
# for fast network connection
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp*.zip
# option 2
# for slow network connection
url=https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/
wget $url -O - -o /dev/null \
| grep taxdmp | perl -ne '/(taxdmp_.+?.zip)/; print "$1\n";' \
| rush -j 2 -v url=$url 'axel -n 5 {url}/{}' \
--immediate-output -c -C download.rush
# --------- unzip ---------
ls taxdmp*.zip | rush -j 1 'unzip {} names.dmp nodes.dmp merged.dmp delnodes.dmp -d {@_(.+)\.}'
# --------- create log ---------
cd ..
taxonkit taxid-changelog -i archive -o taxid-changelog.csv.gz --verbose
Output format (CSV):
# fields comments
taxid # taxid
version # version / time of archive, e.g, 2019-07-01
change # change, values:
# NEW newly added
# REUSE_DEL deleted taxids being reused
# REUSE_MER merged taxids being reused
# DELETE deleted
# MERGE merged into another taxid
# ABSORB other taxids merged into this one
# CHANGE_NAME scientific name changed
# CHANGE_RANK rank changed
# CHANGE_LIN_LIN lineage taxids remain but lineage remain
# CHANGE_LIN_TAX lineage taxids changed
# CHANGE_LIN_LEN lineage length changed
change-value # variable values for changes:
# 1) new taxid for MERGE
# 2) merged taxids for ABSORB
# 3) empty for others
name # scientific name
rank # rank
lineage # full lineage of the taxid
lineage-taxids # taxids of the lineage
# you can use csvtk to investigate them. e.g.,
csvtk grep -f taxid -p 1390515 taxid-changelog.csv.gz
Usage:
taxonkit taxid-changelog [flags]
Flags:
-i, --archive string directory containing decompressed dumped archives
-h, --help help for taxid-changelog
-
Example 1 (E.coli with taxid
562)$ pigz -cd taxid-changelog.csv.gz \ | csvtk grep -f taxid -p 562 \ | csvtk pretty taxid version change change-value name rank lineage lineage-taxids 562 2014-08-01 NEW Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562 562 2014-08-01 ABSORB 662101;662104 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562 562 2015-11-01 ABSORB 1637691 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562 562 2016-10-01 CHANGE_LIN_LIN Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562 562 2018-06-01 ABSORB 469598 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562 # merged taxids $ pigz -cd taxid-changelog.csv.gz \ | csvtk grep -f taxid -p 662101,662104,1637691,469598 \ | csvtk pretty taxid version change change-value name rank lineage lineage-taxids 469598 2014-08-01 NEW Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598 469598 2016-10-01 CHANGE_LIN_LIN Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598 469598 2018-06-01 MERGE 562 Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598 662101 2014-08-01 MERGE 562 662104 2014-08-01 MERGE 562 1637691 2015-04-01 DELETE 1637691 2015-05-01 REUSE_DEL Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691 1637691 2015-11-01 MERGE 562 Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691 -
Example 2 (SARS-CoV-2).
$ time pigz -cd taxid-changelog.csv.gz \ | csvtk grep -f taxid -p 2697049 \ | csvtk pretty taxid version change change-value name rank lineage lineage-taxids 2697049 2020-02-01 NEW Wuhan seafood market pneumonia virus species Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;unclassified Betacoronavirus;Wuhan seafood market pneumonia virus 10239;2559587;76804;2499399;11118;2501931;694002;696098;2697049 2697049 2020-03-01 CHANGE_NAME Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049 2697049 2020-03-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049 2697049 2020-03-01 CHANGE_LIN_LEN Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049 2697049 2020-06-01 CHANGE_LIN_LEN Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049 2697049 2020-07-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 isolate Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049 2697049 2020-08-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049 real 0m7.644s user 0m16.749s sys 0m3.985s -
Example 3 (All subspecies and strain in Akkermansia muciniphila 239935)
# species in Akkermansia $ taxonkit list --show-rank --show-name --indent " " --ids 239935 239935 [species] Akkermansia muciniphila 349741 [strain] Akkermansia muciniphila ATCC BAA-835 # check them all $ pigz -cd taxid-changelog.csv.gz \ | csvtk grep -f taxid -P <(taxonkit list --indent "" --ids 239935) \ | csvtk pretty lineage-taxids taxid version change change-value name rank lineage lineage-taxids 239935 2014-08-01 NEW Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;203557;239934;239935 239935 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;1647988;239934;239935 239935 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935 239935 2016-05-01 ABSORB 1834199 Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935 349741 2014-08-01 NEW Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;203557;239934;239935;349741 349741 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;1647988;239934;239935;349741 349741 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741 349741 2020-07-01 CHANGE_RANK Akkermansia muciniphila ATCC BAA-835 strain cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741
genautocomplete
Usage
Generate shell autocompletion script
Note: The current version supports Bash only.
This should work for *nix systems with Bash installed.
Howto:
1. run: taxonkit genautocomplete
2. create and edit ~/.bash_completion file if you don't have it.
nano ~/.bash_completion
add the following:
for bcfile in ~/.bash_completion.d/* ; do
. $bcfile
done
Usage:
taxonkit genautocomplete [flags]
Flags:
--file string autocompletion file (default "/home/shenwei/.bash_completion.d/taxonkit.sh")
-h, --help help for genautocomplete
--type string autocompletion type (currently only bash supported) (default "bash")