EMBOSS: dbtell

| dbtell

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Display information about a public database

## Description

dbtell displays on-screen information on a database with the specific ID. Optionally, the information may be written to an output file in plain text or HTML.

## Usage

Here is a sample session with dbtell

    % dbtell tsw
    Display information about a public database

    # tsw is defined in special
    # access levels id: Yes query: Yes all: Yes

    DBNAME tsw [
       format:         "swiss"
       method:         "emblcd"
       type:           "Protein protfeatures"
       comment:        "Swissprot native format with EMBL CD-ROM index"
       directory:      "/homes/user/local/share/EMBOSS/test/swiss"
       field:          "id"
       field:          "acc"
       field:          "sv"
       field:          "des"
       field:          "org"
       field:          "key"
       release:        "36"
       edamdat:        "1230 UniProt protein sequence record"
       taxon:          "1 all"
    ]

Go to the input files for this example

## Command line arguments

    Display information about a public database
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-database]          string     The name of the database defined locally for
                                      use by EMBOSS. (Any string)

       Additional (Optional) qualifiers:
       -full               boolean    [N] The default behaviour is to report for
                                      relevant databases only basic information
                                      from the EMBOSS database definition
       -outfile            outfile    [stdout] Output file name

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory         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
[-database] (Parameter 1) | string | The name of the database defined locally for use by EMBOSS. | Any string |
Additional (Optional) qualifiers
-full | boolean | The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition | Boolean value Yes/No | No
-outfile | outfile | Output file name | Output file | stdout
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory | 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

### Input files for usage example

'tsw' is a sequence entry in the example protein database 'tsw'

## Output file format

The output file (plain text format) is an excerpt of and (by default) in the same format as the EMBOSS data file `db.dat`. The format of the file is explained in comments at the top of that file. Optionally, the data can be tabulated.

If the -html qualifier is specified, then the output will be a web page suitable for viewing in any browser.

## Data files

The EMBOSS database information file (`db.dat`) must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.

## Notes

None.

## References

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cachedas | Generate server cache file for DAS servers or for the DAS registry
cachedbfetch | Generate server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch | Generate server cache file for EB-eye search domains
cacheensembl | Generate server cache file for an Ensembl server
servertell | Display information about a public server
showdb | Display information on configured databases
showserver | Display information on configured servers

## Author(s)

Jon Ison
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.

This application was modified by Jon Ison
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