
                                  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: "NUCLEIC COMPOSITION", resulting in the
   reporting of only a tightly restricted set of other programs also
   dealing with the analysis of "NUCLEIC 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: "NUCLEIC", "NUCLEIC COMPOSITION" and "COMPOSITION". All
   programs with the exploded group names which also include "NUCLEIC"
   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 
Finds programs sharing group names
Program to search for: matcher

SEE ALSO
seqmatchall      Does an all-against-all comparison of a set of sequences
supermatcher     Finds a match of a large sequence against one or more sequence
s
water            Smith-Waterman local alignment
wordmatch        Finds all exact matches of a given size between 2 sequences


Command line arguments

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

   Additional (Optional) qualifiers (* if not always prompted):
   -explode            boolean    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
   -outfile            outfile    Output file name
   -html               toggle     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://emboss.sourceforge.net/apps/
                                  programname.html
                                  then if you enter
                                  http://emboss.sourceforge.net/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://emboss.sourceforge.net/apps/
                                  programname.html
                                  then if you enter '.html' here, the second
                                  half of the URL after the program name will
                                  be set.
   -groups             boolean    If you use this option, then only the group
                                  names will output to the file

   Advanced (Unprompted) qualifiers:
   -[no]emboss         boolean    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
   -[no]embassy        boolean    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
   -showembassy        string     If you use this option then this EMBASSY
                                  package program documentation will be
                                  searched. 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
   -colon              boolean    The groups that EMBOSS applications belong
                                  to have up to two levels, for example the
                                  primary group 'ALIGNMENT' has several
                                  sub-groups, or second-level groups, e.g.:
                                  CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
                                  LOCAL, MULTIPLE. To aid programs that parse
                                  the output of seealso that require the names
                                  of these subgroups, a colon ':' will be
                                  placed between the first and second level of
                                  the group name if this option is true.

   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
   [-search]
   (Parameter 1) Enter the name of an EMBOSS program A string of at least
   1 characters Required
   Additional (Optional) qualifiers Allowed values Default
   -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 Boolean value
   Yes/No No
   -outfile Output file name 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. Toggle value 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://emboss.sourceforge.net/apps/
   programname.html then if you enter http://emboss.sourceforge.net/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://emboss.sourceforge.net/apps/
   programname.html then if you enter '.html' 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 Boolean value Yes/No No
   Advanced (Unprompted) 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 Boolean value 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 Boolean value Yes/No Yes
   -showembassy If you use this option then this EMBASSY package program
   documentation will be searched. 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 Any string is accepted An
   empty string is accepted
   -colon The groups that EMBOSS applications belong to have up to two
   levels, for example the primary group 'ALIGNMENT' has several
   sub-groups, or second-level groups, e.g.: CONSENSUS, DIFFERENCES, DOT
   PLOTS, GLOBAL, LOCAL, MULTIPLE. To aid programs that parse the output
   of seealso that require the names of these subgroups, a colon ':' will
   be placed between the first and second level of the group name if this
   option is true. Boolean value Yes/No No

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

   None.

Notes

   None.

References

   None.

Warnings

   None.

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

   None.

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
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   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

   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

   None
