
                               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
