                                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:6.6.0.0

   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
   -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


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

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

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 (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
