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EMBOSS: tfm |
The contributors of the EMBOSS programs do attempt to provide an adequate description of the programs. This documentation is primarily held as HTML pages at http://www.uk.embnet.org/Software/EMBOSS/Apps/
The documentation is also available however through the program tfm as normal text.
tfm is unusual for an EMBOSS program in that it expects to be used interactively and so it displays the documentation text a page at a time, pausing after every page for the user to proess the SPACE bar on their keyboard. (i.e. it uses the UNIX program more to display the information). This behaviour can be turned off by using the qualifier -nomore.
If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@embnet.org).
The unusual name of this program comes from the common computing science expression: RTFM. This acronym, as you probably already know, stands for Read The Fine* Manual; so this is The Fine* Manual.
* Insert the expletive of your choice here!
% tfm wossnameYou will see a page of documentation on the wossname program. To see further pages, you should press the SPACE bar on your keyboard. To stop seeing the documentation before you get to the end of the text, you can press the key q to quit.
Mandatory qualifiers: [-program] string Enter the name of an EMBOSS program Optional qualifiers: -outfile outfile If you enter the name of a file here then this program will write the program names and brief descriptions into that file. -html bool This will format the output for displaying as a WWW document. -more bool This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page. Advanced qualifiers: (none) 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 | |
---|---|---|---|
[-program] (Parameter 1) |
Enter the name of an EMBOSS program | Any string is accepted | An empty string is accepted |
Optional qualifiers | Allowed values | Default | |
-outfile | If you enter the name of a file here then this program will write the program names and brief descriptions into that file. | Output file | stdout |
-html | This will format the output for displaying as a WWW document. | Yes/No | No |
-more | This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page. | Yes/No | @(!$(html)) |
Advanced qualifiers | Allowed values | Default | |
(none) |
The table of command line arguments can be a bit difficult to read. This is the result of changing HTML Web pages to text.
Program name | Description |
---|---|
infoalign | Information on a multiple sequence alignment |
infoseq | Displays some simple information about sequences |
seealso | Finds programs sharing group names |
showdb | Displays information on the currently available databases |
textsearch | Search sequence documentation text. SRS and Entrez are faster! |
whichdb | Search all databases for an entry |
wossname | Finds programs by keywords in their one-line documentation |