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taxgetdown |
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% taxgetdown ttax:9605 -oformat excel Get descendants of taxon(s) Taxon output file [9605.excel]: |
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Go to the output files for this example
Get descendants of taxon(s)
Version: EMBOSS:6.5.6.0
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: (none)
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
-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 | ||||
| (none) | ||||
| 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 | ||||
| -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: 9605 parent: 207598 rank: genus emblprefix: division: 5 divflag: 1 gencode: 1 gcflag: 1 mitocode: 2 mgcflag 1 hidden: 1 nosequence: 1 scientific name: Homo authority: Homo Linnaeus, 1758 |
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.
9606 9605 species Y Homo sapiens 741158 9605 species Y Homo sp. Altai |
| Program name | Description |
|---|---|
| taxget | Get taxon(s) |
| taxgetrank | Get parents 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.