                                   taxget



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Function

   Get taxon(s)

Description

   taxget reads in one or more taxons and writes them out again. 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.

Usage

   Here is a sample session with taxget


% taxget ttax:9606
Get taxon(s)
Taxon output file [9606.tax]:


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

Command line arguments

Get taxon(s)
Version: EMBOSS:6.5.6.0

   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

   '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.tax

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


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
                    taxgetdown    Get descendants of taxon(s)
                    taxgetrank    Get parents 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
