EMBOSS: seealso


Program seealso

Function

Finds programs sharing group names

Description

This program takes the name of an existing program in EMBOSS (or a program in one the associated EMBASSY packages) and gives a list of the programs which share some functionality with it.

It does this by noting the functional groups that the program belongs to and reporting any programs which share those functional groups.

The functional groups of a program are set in the ACD file (this is the part of the program in the EMBOSS system which specifies the required parameters, some help on the parameters, the one-line description of the program, etc.) Normally the names of the groups are fairly specific, such as: "DNA COMPOSITION", resulting in the reporting of only a tightly restricted set of other programs also dealing with the analysis of "DNA COMPOSITION". The '-explode' qualifier will increase the number of groups that the program belongs to by splitting the group name at selected points to produce such groups as: "DNA", "DNA COMPOSITION" and "COMPOSITION". All programs with the exploded group names which also include "DNA" and "COMPOSITION" will now be reported. The result of this qualifier is thus a report of a larger number of programs with a more tenuous link to the specified program. In other words, use the '-explode' qualifier to decrease the specificity of the search.

The groups that the program belongs to can be output by using the '-groups' qualifier.

Usage

Here is a sample session with seealso.

% seealso
Program to search for: matcher
SEE ALSO
simplesw         Simple Smith-Waterman alignment
water            Smith-Waterman local alignment

Command line arguments

   Mandatory qualifiers:
  [-search]            string     Enter the name of an EMBOSS program

   Optional qualifiers (* if not always prompted):
   -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       If you are sending the output to a file,
                                  this will format it for displaying as a
                                  table in a WWW document.
*  -prelink            string     If you are outputting to a file in HTML
                                  format, you can make the program names into
                                  hyper-links by setting this to be the first
                                  half of the URL.
                                  For example, if you wish the program name to
                                  be a hyperlink to the URL:
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps/
                                  programname.shtml
                                  then if you enter
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps/
                                  here, then the first half of the URL before
                                  the program name will be set.
*  -postlink           string     If you are outputting to a file in HTML
                                  format, you can make the program names into
                                  hyper-links by setting this to be the second
                                  half of the URL.
                                  For example, if you wish the program name to
                                  be a hyperlink to the URL:
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps/
                                  programname.shtml
                                  then if you enter '.shtml' here, the second
                                  half of the URL after the program name will
                                  be set.
   -groups             bool       If you use this option, then only the group
                                  names will output to the file
   -explode            bool       The groups that EMBOSS applications belong
                                  to have two forms, exploded and not
                                  exploded. The exploded group names are more
                                  numerous and often vaguely phrased than the
                                  non-exploded ones. The exploded names are
                                  formed from definitions of the group names
                                  that start like NAME1:NAME2 and which are
                                  then expanded into many combinations of the
                                  names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
                                  NAME2 NAME1'. The non-expanded names are
                                  simply like: 'NAME1 NAME2'.
                                  Using expanded group names will find many
                                  more programs which share at least some of
                                  the expanded names than using the
                                  non-exploded names and so you will get more
                                  programs reported as sharing a similar
                                  function than you will if you specify that
                                  you wish to use non-exploded names

   Advanced qualifiers:
   -[no]emboss         bool       If you use this option then EMBOSS program
                                  documentation will be searched. If this
                                  option is set to be false, then only the
                                  EMBASSY programs will be searched (if the
                                  -embassy option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence scheme, ie. they
                                  may wish to charge money for them.
   -[no]embassy        bool       If you use this option then EMBASSY program
                                  documentation will be searched. If this
                                  option is set to be false, then only the
                                  EMBOSS programs will be searched (if the
                                  -emboss option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence scheme, ie. they
                                  may wish to charge money for them.


Mandatory qualifiers Allowed values Default
[-search]
(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 If you are sending the output to a file, this will format it for displaying as a table in a WWW document. Yes/No No
-prelink If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.shtml then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the program name will be set. Any string is accepted An empty string is accepted
-postlink If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.shtml then if you enter '.shtml' here, the second half of the URL after the program name will be set. Any string is accepted An empty string is accepted
-groups If you use this option, then only the group names will output to the file Yes/No No
-explode The groups that EMBOSS applications belong to have two forms, exploded and not exploded. The exploded group names are more numerous and often vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The non-expanded names are simply like: 'NAME1 NAME2'. Using expanded group names will find many more programs which share at least some of the expanded names than using the non-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non-exploded names Yes/No No
Advanced qualifiers Allowed values Default
-[no]emboss If you use this option then EMBOSS program documentation will be searched. If this option is set to be false, then only the EMBASSY programs will be searched (if the -embassy option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme, ie. they may wish to charge money for them. Yes/No Yes
-[no]embassy If you use this option then EMBASSY program documentation will be searched. If this option is set to be false, then only the EMBOSS programs will be searched (if the -emboss option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme, ie. they may wish to charge money for them. Yes/No Yes

Input file format

Output file format

The result is header line 'SEE ALSO' then a simple list of program names followed by the one-line description of the program.

If the '-html' qualifier is used, then the result is an HTML-formatted table, lacking the HTML document structures such as <HTML>, <BODY>, </BODY>, </HTML> which the user is expected to provide as the table will usually be included in the middle of a larger HTML document.

Data files

 

Notes

 

References

 

Warnings

 

Diagnostic Error Messages

The error message:

FATAL ERROR: No application specified.

is output if a non-existent program name is specified.

Exit status

The program exits with exist status '0' unless a non-existent program name is specified, when the exit status is '1'.

Known bugs

 

See also

Program nameDescription
wossnameFinds programs by keywords in their one-line documentation

Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

History

Written 16 June 2000 in response to a need to improve the automatic construction of EMBOSS documentation web pages.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments