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taxgetrank |
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% taxgetrank ttax:9606 -oformat excel
Get parents of taxon(s)
Taxonomic rank(s)
kingdom : Kingdom
phylum : Phylum
class : Class
order : Order
family : Family
genus : Genus
species : Species
tribe : Tribe
varietas : varietas
species group : Species group
species subgroup : Species subgroup
no rank : None
superkingdom : Superkingdom
superphylum : Superphylum
superclass : Superclass
superorder : Superorder
superfamily : Superfamily
subkingdom : Subkingdom
subphylum : Subphylum
subclass : Subclass
suborder : Suborder
subfamily : Subfamily
subgenus : Subgenus
subspecies : Subspecies
subtribe : Subtribe
infraclass : Infraclass
infraorder : Infraorder
parvorder : Parvorder
Find taxons at rank [kingdom,phylum,class,order,family,genus,species]:
Taxon output file [9606.excel]:
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Go to the input files for this example
Go to the output files for this example
Example 2
% taxgetrank ttax:9606 -oformat excel
Get parents of taxon(s)
Taxonomic rank(s)
kingdom : Kingdom
phylum : Phylum
class : Class
order : Order
family : Family
genus : Genus
species : Species
tribe : Tribe
varietas : varietas
species group : Species group
species subgroup : Species subgroup
no rank : None
superkingdom : Superkingdom
superphylum : Superphylum
superclass : Superclass
superorder : Superorder
superfamily : Superfamily
subkingdom : Subkingdom
subphylum : Subphylum
subclass : Subclass
suborder : Suborder
subfamily : Subfamily
subgenus : Subgenus
subspecies : Subspecies
subtribe : Subtribe
infraclass : Infraclass
infraorder : Infraorder
parvorder : Parvorder
Find taxons at rank [kingdom,phylum,class,order,family,genus,species]: *
Taxon output file [9606.excel]:
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Go to the output files for this example
Example 3
% taxgetrank ttax:9606 -oformat excel -hidden
Get parents of taxon(s)
Taxonomic rank(s)
kingdom : Kingdom
phylum : Phylum
class : Class
order : Order
family : Family
genus : Genus
species : Species
tribe : Tribe
varietas : varietas
species group : Species group
species subgroup : Species subgroup
no rank : None
superkingdom : Superkingdom
superphylum : Superphylum
superclass : Superclass
superorder : Superorder
superfamily : Superfamily
subkingdom : Subkingdom
subphylum : Subphylum
subclass : Subclass
suborder : Suborder
subfamily : Subfamily
subgenus : Subgenus
subspecies : Subspecies
subtribe : Subtribe
infraclass : Infraclass
infraorder : Infraorder
parvorder : Parvorder
Find taxons at rank [kingdom,phylum,class,order,family,genus,species]: *
Taxon output file [9606.excel]:
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Go to the output files for this example
Get parents of taxon(s)
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-taxons] taxon Taxon filename and optional format, or
reference (input query)
[-rank] menu [kingdom,phylum,class,order,family,genus,species]
Multiple ranks can be specified, or '*' for
all (Values: kingdom (Kingdom); phylum
(Phylum); class (Class); order (Order);
family (Family); genus (Genus); species
(Species); tribe (Tribe); varietas
(varietas); species group (Species group);
species subgroup (Species subgroup); no rank
(None); superkingdom (Superkingdom);
superphylum (Superphylum); superclass
(Superclass); superorder (Superorder);
superfamily (Superfamily); subkingdom
(Subkingdom); subphylum (Subphylum);
subclass (Subclass); suborder (Suborder);
subfamily (Subfamily); subgenus (Subgenus);
subspecies (Subspecies); subtribe
(Subtribe); infraclass (Infraclass);
infraorder (Infraorder); parvorder
(Parvorder))
[-outfile] outtaxon (no help text) outtaxon value
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-hidden boolean [N] Show taxons hidden in GenBank
Associated qualifiers:
"-taxons" associated qualifiers
-iformat1 string Input taxonomy format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-idbname1 string User-provided database name
"-outfile" associated qualifiers
-odirectory3 string Output directory
-oformat3 string Taxonomy output format
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
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| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| [-taxons] (Parameter 1) |
taxon | Taxon filename and optional format, or reference (input query) | NCBI taxonomy entries | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| [-rank] (Parameter 2) |
list | Multiple ranks can be specified, or '*' for all |
|
kingdom,phylum,class,order,family,genus,species | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 3) |
outtaxon | (no help text) outtaxon value | NCBI taxonomy entries | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| (none) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -hidden | boolean | Show taxons hidden in GenBank | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| "-taxons" associated taxon qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -iformat1 -iformat_taxons |
string | Input taxonomy format | Any string | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -iquery1 -iquery_taxons |
string | Input query fields or ID list | Any string | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -ioffset1 -ioffset_taxons |
integer | Input start position offset | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -idbname1 -idbname_taxons |
string | User-provided database name | Any string | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| "-outfile" associated outtaxon qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -odirectory3 -odirectory_outfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -oformat3 -oformat_outfile |
string | Taxonomy output format | Any string | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| General qualifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The input is a standard EMBOSS taxonomy query.
The expected source of taxonomy information is the NCBI Taxonomy database "taxon" which is available as a standard database in all EMBOSS installations.
Data can also be read from taxonomy output in "ncbi" format written by an EMBOSS application.
See: http://emboss.sf.net/docs/themes/TaxonFormats.html for further information on taxon formats.
id: 9606 parent: 9605 rank: species emblprefix: HS division: 5 divflag: 1 gencode: 1 gcflag: 1 mitocode: 2 mgcflag 1 hidden: 1 nosequence: 1 scientific name: Homo sapiens authority: Homo sapiens Linnaeus, 1758 genbank common name: human common name: man |
The results can be output in one of several styles by using the command-line qualifier -oformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: ncbi, ebi, tax, excel.
See: http://emboss.sf.net/docs/themes/TaxonFormats.html for further information on taxon formats.
9605 207598 genus N Homo 9604 314295 family N Hominidae 9443 314146 order N Primates 40674 32524 class N Mammalia 7711 33511 phylum N Chordata 33208 33154 kingdom N Metazoa |
9605 207598 genus N Homo 9604 314295 family N Hominidae 9526 314293 parvorder N Catarrhini 376913 9443 suborder N Haplorrhini 9443 314146 order N Primates 314146 9347 superorder N Euarchontoglires 9347 32525 no rank N Eutheria 40674 32524 class N Mammalia 117571 117570 no rank N Euteleostomi 7742 89593 no rank N Vertebrata 89593 7711 subphylum N Craniata 7711 33511 phylum N Chordata 33208 33154 kingdom N Metazoa 2759 131567 superkingdom N Eukaryota |
9605 207598 genus N Homo 207598 9604 subfamily Y Homininae 9604 314295 family N Hominidae 314295 9526 superfamily Y Hominoidea 9526 314293 parvorder N Catarrhini 314293 376913 infraorder Y Simiiformes 376913 9443 suborder N Haplorrhini 9443 314146 order N Primates 314146 9347 superorder N Euarchontoglires 9347 32525 no rank N Eutheria 32525 40674 no rank Y Theria 40674 32524 class N Mammalia 32524 32523 no rank Y Amniota 32523 8287 no rank Y Tetrapoda 8287 117571 no rank Y Sarcopterygii 117571 117570 no rank N Euteleostomi 117570 7776 no rank Y Teleostomi 7776 7742 superclass Y Gnathostomata 7742 89593 no rank N Vertebrata 89593 7711 subphylum N Craniata 7711 33511 phylum N Chordata 33511 33316 no rank Y Deuterostomia 33316 33213 no rank Y Coelomata 33213 6072 no rank Y Bilateria 6072 33208 no rank Y Eumetazoa 33208 33154 kingdom N Metazoa 33154 2759 no rank Y Fungi/Metazoa group 2759 131567 superkingdom N Eukaryota 131567 1 no rank Y cellular organisms |
| Program name | Description |
|---|---|
| taxget | Get taxon(s) |
| taxgetdown | Get descendants of taxon(s) |
| taxgetspecies | Get all species under taxon(s) |
| taxgetup | Get parents of taxon(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.