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:6.5.0.0

   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