EMBOSS: showdb

| ## EMBOSS: showdb

# Program showdb

## Function

Displays information on the currently available databases

## Description

This writes out a simple table displaying the names, contents and available ways of accessing the sequence databases.

The available ways of accessing the databases are 'ID', 'Query' and 'All'. These refer to the way that you can search the databases to get entries from them, which is governed by the ways the database has been set up and the way it is organised and indexed.

Different databases may have different access capabilities, depending on how your local site is organised.

EMBOSS has been designed to be extremely flexible in its use of sequence databases formats, so that it is easy to set EMBOSS up to use your site's existing databases. Sometimes this means that it is hard to extract entries from some databases in particular ways. For example, a flat file database with no index is only useful for reading all entries, while a database located in another site that is available via the WWW may only provide single entries.

'ID' (also known as 'single entry') allows the programs to extract a single explicitly named entry from the database, for example embl:x13776

'Query' (also known as 'wild') indicates that programs can extract a set of matching wildcard entry names (this may be slow for some methods of access). For example you can look at all of the human PAX proteins in SWISS_PROT by: swissprot:pax*_human

'All' allows the programs to analyse all the entries in the database sequentially. For example this lets you look at all entries in the database with the notation: embl:*

A database may have several different methods of access available. Ideally all of the databases available on your site will be available in all three ways, but this is not the best of all posssible worlds and so you might like to check how you can access the databases by running this program and having a look.

## Usage

Display information on the currently available databases:

    % showdb

Write out the display to a file:

    % showdb -outfile showdb.out

Display information on one explicit database:

    % showdb -database swissprot

Display information on the databases formatted for inclusion in HTML:

    % showdb -html

Display protein databases only:

    % showdb -nonucleic

Display the information with no headings

    % showdb -noheading

Display just a list of the available database names

    % showdb -noheading -notype -noid -noquery -noall -nocomment -auto

Display only the names and types

    % showdb -only -type

## Command line arguments

       Mandatory qualifiers: (none)
       Optional qualifiers:
       -database           string     Name of a single database to give
                                      information on
       -html               bool       Format output as an HTML table
       -[no]protein        bool       Display protein databases
       -[no]nucleic        bool       Display nucleic acid databases
       -release            bool       Display 'release' column
       -outfile            outfile    If you enter the name of a file here then
                                      this program will write the database details
                                      into that file.

       Advanced qualifiers:
       -only               bool       This is a way of shortening the command line
                                      if you only want a few things to be
                                      displayed. Instead of specifying:
                                      '-nohead -notype -noid -noquery -noall'
                                      to get only the comment output, you can
                                      specify
                                      '-only -comment'
       -heading            bool       Display column headings
       -type               bool       Display 'type' column
       -id                 bool       Display 'id' column
       -query              bool       Display 'qry' column
       -all                bool       Display 'all' column
       -comment            bool       Display 'comment' column

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
(none)
Optional qualifiers | Allowed values | Default
-database | Name of a single database to give information on | Any string is accepted | An empty string is accepted
-html | Format output as an HTML table | Yes/No | No
-[no]protein | Display protein databases | Yes/No | Yes
-[no]nucleic | Display nucleic acid databases | Yes/No | Yes
-release | Display 'release' column | Yes/No | No
-outfile | If you enter the name of a file here then this program will write the database details into that file. | Output file | stdout
Advanced qualifiers | Allowed values | Default
-only | This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' | Yes/No | No
-heading | Display column headings | Yes/No | @(!$(only))
-type | Display 'type' column | Yes/No | @(!$(only))
-id | Display 'id' column | Yes/No | @(!$(only))
-query | Display 'qry' column | Yes/No | @(!$(only))
-all | Display 'all' column | Yes/No | @(!$(only))
-comment | Display 'comment' column | Yes/No | @(!$(only))

## Input file format

None.

## Output file format

The output is a simple table, e.g.:

    ------------------------------------------------------------------------------
    # Name        Type ID  Qry All Comment
    # ====        ==== ==  === === =======
    swissprot     P    OK  OK  OK  -
    sw            P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
    em            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
    ------------------------------------------------------------------------------

Type 'P' indicates that this is a Protein database.

Type 'N' indicates that this is a Nucleic database.

'OK' under ID, Qry or All indicates that that access method can be used on this database. A '-' indicates that you cannot access this database in that way.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.

## Data files

The databases are specified in the files "emboss.defaults" for site wide definitions, and "~/.embossrc" for the user's own settings.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

"The database 'xyz' does not exist" You have supplied the name of a database with the -database qualifier, but that database does not exist as far as EMBOSS is concerned.

## Exit status

It always exits with status 0, unless the above diagnostic message is displayed.

## Known bugs

None noted.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
cirdna | Draws circular maps of DNA constructs
infoalign | Information on a multiple sequence alignment
infoseq | Displays some simple information about sequences
lindna | Draws linear maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showfeat | Show features of a sequence
showseq | Display a sequence with features, translation etc
textsearch | Search sequence documentation text. SRS and Entrez are faster!
tfm | Displays a program's help documentation manual
whichdb | Search all databases for an entry
wossname | Finds programs by keywords in their one-line documentation

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Completed 6th August 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments