|   | 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]: 
 | 
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]: 
 | 
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]: 
 | 
Go to the output files for this example
| 
Get parents of taxon(s)
Version: EMBOSS:6.6.0.0
   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
 | 
| 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.