                                  ontocount



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Count ontology term(s)

Description

   ontocount reads ontology entries and reports the number of entries
   found.

Usage

   Here is a sample session with ontocount


% ontocount edam:1234
Count ontology term(s)
Output file [stdout]:

1


   Go to the input files for this example

   Example 2


% ontocount edam:1234 -subclasses
Count ontology term(s)
Output file [stdout]:

5


Command line arguments

Count ontology term(s)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-oboterms]          obo        Obo term filename and optional format, or
                                  reference (input query)
  [-outfile]           outfile    [stdout] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations
                                  (sub-classes) of the matched terms.
   -obsolete           boolean    [N] The default behaviour is to not use or
                                  return obsolete terms. This option if set
                                  will include all terms.

   Associated qualifiers:

   "-oboterms" associated qualifiers
   -iformat1           string     Input obo 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

   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 ontology query.

   The major ontology sources defined as standard in EMBOSS installations
   are EDAM, GO (gene Ontology) and SO (Sequence Ontology).

   Data can also be read from ontology output in "obo" format written by
   an EMBOSS application.

  Input files for usage example

  Database entry: edam:1234

[Term]
id: EDAM_data:1234
name: Sequence set (nucleic acid)
namespace: data
def: Any collection of multiple nucleotide sequences and associated metadata tha
t do not (typically) correspond to common sequence database records or database
entries.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence


Output file format

   ontocount reports the number of ontology terms read.

Data files

   None.

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
                    ontoget         Get ontology term(s)
                    ontogetcommon   Get common ancestor for terms
                    ontogetdown     Get ontology term(s) by parent id
   ontogetobsolete  Get ontology ontology terms
                    ontogetroot     Get ontology root terms by child identifier
                    ontogetsibs     Get ontology term(s) by id with common parent
                    ontogetup       Get ontology term(s) by id of child
                    ontoisobsolete  Report whether an ontology term id is obsolete
                    ontotext        Get ontology term(s) original full text

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
