ontocount

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Function

Description

Usage

% ontocount edam:0001234 Count ontology term(s) Output file [stdout]: 1

Go to the input files for this example

Example 2

% ontocount edam:0001234 -subclasses Count ontology term(s) Output file [stdout]: 7

Command line arguments

Count ontology term(s)
Version: EMBOSS:6.4.0.0

   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
   -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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-oboterms] (Parameter 1)	obo	Obo term filename and optional format, or reference (input query)	OBO bio-ontology term(s)
[-outfile] (Parameter 2)	outfile	Output file name	Output file	stdout
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-subclasses	boolean	Extend the query matches to include all terms which are specialisations (sub-classes) of the matched terms.	Boolean value Yes/No	No
-obsolete	boolean	The default behaviour is to not use or return obsolete terms. This option if set will include all terms.	Boolean value Yes/No	No
Associated qualifiers
"-oboterms" associated obo qualifiers
-iformat1 -iformat_oboterms	string	Input obo format	Any string
-idbname1 -idbname_oboterms	string	User-provided database name	Any string
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	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 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:0001234

[Term]
id: EDAM:0001234
name: Sequence set (nucleic acid)
namespace: data
def: Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
subset: data
is_a: EDAM:0000850 ! Sequence set
is_a: EDAM:0002977 ! Nucleic acid sequence

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

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