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:6.5.0.0

   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 (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)
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

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 © 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