taxgetup |
Please help by correcting and extending the Wiki pages.
% taxgetup ttax:9606 -oformat excel Get parents of taxon(s) Taxon output file [9606.excel]: |
Go to the input files for this example
Go to the output files for this example
Example 2
% taxgetup ttax:9606 -hidden -oformat excel Get parents of taxon(s) Taxon output file [9606.excel]: |
Go to the output files for this example
Get parents of taxon(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-taxons] taxon Taxon filename and optional format, or reference (input query) [-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 -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 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 |
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 | |
[-outfile] (Parameter 2) |
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 | |
-idbname1 -idbname_taxons |
string | User-provided database name | Any string | |
"-outfile" associated outtaxon qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
-oformat2 -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 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) |
taxgetrank | Get parents of taxon(s) |
taxgetspecies | Get all species under taxon(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.