                                 taxgetrank



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Function

   Get parents of taxon(s)

Description

   taxgetrank reads in one or more taxons, and reports the taxons at each
   level from the current to the top. The taxon input may be a literal
   sequence or read from a database, file, file of taxon names, or even
   the command-line or the output of another programs. The taxon output
   can be written to screen, to file, or passed to another program. A wide
   range of standard taxon formats may be specified for input and output.

Algorithm

   The NCBI taxonomy records the parent of each taxon, up to a known top
   level 1.

Usage

   Here is a sample session with taxgetrank


% 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

Command line arguments

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,speci
es]
                                  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


Input file format

   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.

  Input files for usage example

   'ttax:9606' is a sequence entry in the example taxonomy database 'ttax'

  Database entry: ttax:9606

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


Output file format

   The output is a standard EMBOSS taxon file.

   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.

  Output files for usage example

  File: 9606.excel

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

  Output files for usage example 2

  File: 9606.excel

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

  Output files for usage example 3

  File: 9606.excel

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

Data files

   The NCBI Taxonomy Ontology is included in EMBOSS as local database
   taxon.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                    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)

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.

Comments

                    None
