                                   dbtell



Wiki

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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


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 (c) 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 (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
