
                                  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

   Here is a sample session with showdb

   Display information on the currently available databases:


% showdb 
Displays information on the currently available databases

# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
qapblast      P    OK  OK  OK  BLAST swissnew
qapblastall   P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta      P    OK  OK  OK  FASTA file swissnew entries
qapflat       P    OK  OK  OK  Swissnew flatfiles
qapflatall    P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc    P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc    P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir         P    OK  OK  OK  PIR
qapirall      P    OK  OK  OK  PIR
qapirinc      P    OK  OK  OK  PIR
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with EMBL C
D-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qanfasta      N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall   N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat       N    OK  OK  OK  EMBL flatfiles
qangcg        N    OK  OK  OK  GCG format EMBL
qangcgall     N    OK  OK  OK  GCG format EMBL
qangcgexc     N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc     N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc      N    OK  OK  OK  PIR
qasrs         N    OK  OK  -   EMBL in local srs installation
qasrsfasta    N    OK  OK  -   EMBL in local srs installation, fasta format
qasrswww      N    OK  -   -   Remote SRS web server
qawfasta      N    OK  OK  OK  FASTA file wormpep entries
tembl         N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest     N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
tgb           N    OK  -   -   Genbank IDs
tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

   Example 2

   Write the results to a file:


% showdb -outfile showdb.out 
Displays information on the currently available databases

   Go to the output files for this example

   Example 3

   Display information on one explicit database:


% showdb -database tsw 
Displays information on the currently available databases

# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index

   Go to the input files for this example

   Example 4

   Display information on the databases formatted in HTML:


% showdb -html 
Displays information on the currently available databases


 Name Type ID Qry All Comment

 qapblast P OK   OK   OK   BLAST swissnew

 qapblastall P OK   OK   OK   BLAST swissnew, all fields indexed

 qapblastsplit P OK   OK   OK   BLAST swissnew split in 5 files

 qapblastsplitexc P OK   OK   OK   BLAST swissnew split in 5 files, not file 02

 qapblastsplitinc P OK   OK   OK   BLAST swissnew split in 5 files, only file 0
2

 qapfasta P OK   OK   OK   FASTA file swissnew entries

 qapflat P OK   OK   OK   Swissnew flatfiles

 qapflatall P OK   OK   OK   Swissnew flatfiles, all fields indexed

 qapflatexc P OK   OK   OK   Swissnew flatfiles, no updated sequence file

 qapflatinc P OK   OK   OK   Swissnew flatfiles, only updated sequence file

 qapir P OK   OK   OK   PIR

 qapirall P OK   OK   OK   PIR

 qapirinc P OK   OK   OK   PIR

 tpir P OK   OK   OK   PIR using NBRF access for 4 files

 tsw P OK   OK   OK   Swissprot native format with EMBL CD-ROM index

 tswnew P OK   OK   OK   Swissnew as 3 files in native format with EMBL CD-ROM
index

 twp P OK   OK   OK   EMBL new in native format with EMBL CD-ROM index

 qanfasta N OK   OK   OK   FASTA file EMBL rodents

 qanfastaall N OK   OK   OK   FASTA file EMBL rodents, all fields indexed

 qanflat N OK   OK   OK   EMBL flatfiles

 qangcg N OK   OK   OK   GCG format EMBL

 qangcgall N OK   OK   OK   GCG format EMBL

 qangcgexc N OK   OK   OK   GCG format EMBL without prokaryotes

 qangcginc N OK   OK   OK   GCG format EMBL only prokaryotes

 qapirexc N OK   OK   OK   PIR

 qasrs N OK   OK   -    EMBL in local srs installation

 qasrsfasta N OK   OK   -    EMBL in local srs installation, fasta format

 qasrswww N OK   -    -    Remote SRS web server

 qawfasta N OK   OK   OK   FASTA file wormpep entries

 tembl N OK   OK   OK   EMBL in native format with EMBL CD-ROM index

 temblall N -    -    OK   EMBL in native format with EMBL CD-ROM index

 temblrest N -    -    OK   EMBL in native format with EMBL CD-ROM index

 temblvrt N -    -    OK   EMBL in native format with EMBL CD-ROM index

 tgb N OK   -    -    Genbank IDs

 tgenbank N OK   OK   OK   GenBank in native format with EMBL CD-ROM index



   Example 5

   Display protein databases only:


% showdb -nonucleic 
Displays information on the currently available databases

# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
qapblast      P    OK  OK  OK  BLAST swissnew
qapblastall   P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta      P    OK  OK  OK  FASTA file swissnew entries
qapflat       P    OK  OK  OK  Swissnew flatfiles
qapflatall    P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc    P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc    P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir         P    OK  OK  OK  PIR
qapirall      P    OK  OK  OK  PIR
qapirinc      P    OK  OK  OK  PIR
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with EMBL C
D-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index

   Example 6

   Display the information with no headings:


% showdb -noheading 
Displays information on the currently available databases

qapblast      P    OK  OK  OK  BLAST swissnew
qapblastall   P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta      P    OK  OK  OK  FASTA file swissnew entries
qapflat       P    OK  OK  OK  Swissnew flatfiles
qapflatall    P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc    P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc    P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir         P    OK  OK  OK  PIR
qapirall      P    OK  OK  OK  PIR
qapirinc      P    OK  OK  OK  PIR
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with EMBL C
D-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qanfasta      N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall   N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat       N    OK  OK  OK  EMBL flatfiles
qangcg        N    OK  OK  OK  GCG format EMBL
qangcgall     N    OK  OK  OK  GCG format EMBL
qangcgexc     N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc     N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc      N    OK  OK  OK  PIR
qasrs         N    OK  OK  -   EMBL in local srs installation
qasrsfasta    N    OK  OK  -   EMBL in local srs installation, fasta format
qasrswww      N    OK  -   -   Remote SRS web server
qawfasta      N    OK  OK  OK  FASTA file wormpep entries
tembl         N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest     N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
tgb           N    OK  -   -   Genbank IDs
tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

   Example 7

   Display just a list of the available database names:


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

qapblast
qapblastall
qapblastsplit
qapblastsplitexc
qapblastsplitinc
qapfasta
qapflat
qapflatall
qapflatexc
qapflatinc
qapir
qapirall
qapirinc
tpir
tsw
tswnew
twp
qanfasta
qanfastaall
qanflat
qangcg
qangcgall
qangcgexc
qangcginc
qapirexc
qasrs
qasrsfasta
qasrswww
qawfasta
tembl
temblall
temblrest
temblvrt
tgb
tgenbank

   Example 8

   Display only the names and types:


% showdb -only -type 
Displays information on the currently available databases

qapblast      P
qapblastall   P
qapblastsplit P
qapblastsplitexc P
qapblastsplitinc P
qapfasta      P
qapflat       P
qapflatall    P
qapflatexc    P
qapflatinc    P
qapir         P
qapirall      P
qapirinc      P
tpir          P
tsw           P
tswnew        P
twp           P
qanfasta      N
qanfastaall   N
qanflat       N
qangcg        N
qangcgall     N
qangcgexc     N
qangcginc     N
qapirexc      N
qasrs         N
qasrsfasta    N
qasrswww      N
qawfasta      N
tembl         N
temblall      N
temblrest     N
temblvrt      N
tgb           N
tgenbank      N

Command line arguments

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on
   -html               boolean    Format output as an HTML table
   -[no]protein        boolean    Display protein databases
   -[no]nucleic        boolean    Display nucleic acid databases
   -fields             boolean    This displays the search fields that can be
                                  used on this database, other than the
                                  standard 'id' or 'acc' fields.
   -release            boolean    Display 'release' column
   -outfile            outfile    Output file name

   Advanced (Unprompted) qualifiers:
   -only               boolean    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            boolean    Display column headings
   -type               boolean    Display 'type' column
   -id                 boolean    Display 'id' column
   -query              boolean    Display 'qry' column
   -all                boolean    Display 'all' column
   -comment            boolean    Display 'comment' column

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory          string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write 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. 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   (none)
   Additional (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 Boolean value Yes/No No
   -[no]protein Display protein databases Boolean value Yes/No Yes
   -[no]nucleic Display nucleic acid databases Boolean value Yes/No Yes
   -fields This displays the search fields that can be used on this
   database, other than the standard 'id' or 'acc' fields. Boolean value
   Yes/No No
   -release Display 'release' column Boolean value Yes/No No
   -outfile Output file name Output file stdout
   Advanced (Unprompted) 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' Boolean value Yes/No No
   -heading Display column headings Boolean value Yes/No @(!$(only))
   -type Display 'type' column Boolean value Yes/No @(!$(only))
   -id Display 'id' column Boolean value Yes/No @(!$(only))
   -query Display 'qry' column Boolean value Yes/No @(!$(only))
   -all Display 'all' column Boolean value Yes/No @(!$(only))
   -comment Display 'comment' column Boolean value Yes/No @(!$(only))

Input file format

   None.

  Input files for usage example 3

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

Output file format

  Output files for usage example 2

  File: showdb.out

# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
qapblast      P    OK  OK  OK  BLAST swissnew
qapblastall   P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta      P    OK  OK  OK  FASTA file swissnew entries
qapflat       P    OK  OK  OK  Swissnew flatfiles
qapflatall    P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc    P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc    P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir         P    OK  OK  OK  PIR
qapirall      P    OK  OK  OK  PIR
qapirinc      P    OK  OK  OK  PIR
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with EMBL C
D-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qanfasta      N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall   N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat       N    OK  OK  OK  EMBL flatfiles
qangcg        N    OK  OK  OK  GCG format EMBL
qangcgall     N    OK  OK  OK  GCG format EMBL
qangcgexc     N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc     N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc      N    OK  OK  OK  PIR
qasrs         N    OK  OK  -   EMBL in local srs installation
qasrsfasta    N    OK  OK  -   EMBL in local srs installation, fasta format
qasrswww      N    OK  -   -   Remote SRS web server
qawfasta      N    OK  OK  OK  FASTA file wormpep entries
tembl         N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest     N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt      N    -   -   OK  EMBL in native format with EMBL CD-ROM index
tgb           N    OK  -   -   Genbank IDs
tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

   The output is a simple table.

   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.

   Note that 'OK' does not mean that the database is working correctly.
   It simply means that showdb has read the database definition correctly
   and that this method of access to the database should be possible.

   If you are setting up a new database, then you should check that it
   works correctly by extracting entries from it using seqret.

   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

   Note that 'OK' in the output does not mean that the database is
   working correctly. It simply means that showdb has read the database
   definition correctly and that this method of access to the database
   should be possible.

   If you are setting up a new database, then you should check that it
   works correctly by extracting entries from it using seqret.

   You can set up your own private databases by editing a file called
   '.embossrc' to contain database specifications.

   You can set up public databases by editing the file
   '/usr/local/share/EMBOSS/emboss.default' (if you have the permission
   to do this).

   The 'emboss.default' file will already have the definitions of the
   test databases in: tsw, tembl, tpir, etc. These are the databases that
   are used in the examples shown in the documentation of the programs.

   For details of the database definitions, you should first read David's
   Administration Guide: http://emboss.sourceforge.net/docs/adminguide/
   especially:
   http://emboss.sourceforge.net/docs/adminguide/adminguide/node4.html 

   See also: http://emboss.sourceforge.net/docs/themes/Databases.html for
   a lot of detail of the syntax of database definition.

   Just because showdb can display the database definitions, it does NOT
   mean that the databases are set up correctly. You must now test them
   using seqret.

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
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   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)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

   None
