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