taxgetspecies

 

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Function

Get all species under taxon(s)

Description

taxgetspecies reads in one or more taxons, finds all taxons below in the hierarchy, and writes out any at the species level. 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 taxgetspecies 


% taxgetspecies taxon-tax:hominidae -oformat excel 
Get all species under taxon(s)
Taxon output file [9604.excel]:

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Get all species under 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: (none)
   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
(none)
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

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

Database entry: taxon-tax:hominidae

id: 9604
parent: 314295
rank: family
emblprefix: 
division: 5
divflag: 1
gencode: 1
gcflag: 1
mitocode: 2
mgcflag 1
hidden: 1
nosequence: 1
scientific name: Hominidae
authority: Hominidae Gray, 1825
synonym: Pongidae
common name: great apes

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: 9604.excel

9600	9599	species	Y	Pongo pygmaeus
9601	9599	species	Y	Pongo abelii
9603	9599	species	Y	Pongo sp.
502961	9599	species	Y	Pongo abelii x pygmaeus
499232	9592	species	Y	Gorilla beringei
9593	9592	species	Y	Gorilla gorilla
9597	9596	species	Y	Pan paniscus
9598	9596	species	Y	Pan troglodytes
317028	9596	species	Y	Pan sp. WO2005014654
445518	9596	species	Y	Pan sp. WO2007026120
741158	9605	species	Y	Homo sp. Altai
9606	9605	species	Y	Homo sapiens

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)
taxgetrank Get parents of 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