Module Detail Information

Name:ShowDB
Type: Module
Short URL:
http://bit.ly/1B7Eg47
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.
Executable:
/showdb
Input Parameters:
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Version
 - Input Database
 - HTML
 - Display Protein Databases
 - Display Nucleic Acid Databases
 - Display All Columns
 - Display Access Methods
 - Display Search Fields
 - Display Short Name
 - Display Release Column
 - Shorten Command Line
 - Display column headings
 - Display type Column
 - Display ID column
 - Display qry Column
 - Display all Column
 - Display comment Column
Output Parameters:
 - Output File
 - Output Directory
File size:26.37 KB
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