
                             EMBOSS: embossdata
     _________________________________________________________________
   
                              Program embossdata
                                       
Function

   Finds or fetches the data files read in by the EMBOSS programs
   
Description

   This is a utility to indicate which directories can hold EMBOSS data
   files and what the names of these files are.
   
   The names of EMBOSS data files all start with the character 'E', by
   convention, to distinguish them somewhat from any other files,
   especially files in your home directory.
   
   EMBOSS data files are read in by assorted EMBOSS programs, for example
   the files holding the various genetic codes to translate from nucleic
   acid codons to amino acids are held in files called "EGC.0", "EGC.1",
   "EGC.2", etc. These files normally are kept in a standard data
   directory under the EMBOSS package installation position:
   ".../emboss/emboss/data/". When EMBOSS programs require a data file,
   they search for it, in order, through the following set of
   directories:
     * The current directory
     * '.embossdata' in the current directory
     * Your home directory
     * '.embossdata' in your home directory
     * The EMBOSS standard data directory
       
   If a data file is placed in the current directory, EMBOSS programs
   will use it in preference to the file of the same name in the EMBOSS
   standard data directory. Thus if you wish to modify a data file to
   change the behaviour of an EMBOSS program, you should obtain it from
   the EMBOSS standard data directory, edit it, and place it in one of
   the other directories, such as the current directory or your home
   directory.
   
   The program embossdata is a utility to enable you to check on the
   location of the directories which could hold data files, to display
   the names of data files in those directories and to make local copies
   of the data files from the EMBOSS standard data directory in order for
   you to modify them.
   
Usage

   Display the directories searched for EMBOSS data files:
% embossdata

   Display the names of data file in all of the possible data
   directories:
% embossdata -showall

   Display the directories which contain a particular EMBOSS data file:
% embossdata -filename EPAM60

   Make a copy of an EMBOSS data file in the current directory:
% embossdata -fetch -filename Epepcoil.dat

Command line arguments

   Mandatory qualifiers (* if not always prompted):
*  -filename           string     This specifies the name of the file that
                                  should be fetched into the current directory
                                  or searched for in all of the directories
                                  that EMBOSS programs search when looking for
                                  a data file. The name of the file is not
                                  altered when it is fetched.

   Optional qualifiers (* if not always prompted):
   -showall            bool       Show all potential EMBOSS data files
*  -fetch              bool       Fetch a data file
   -outf               outfile    This specifies the name of the file that the
                                  results of a search for a file in the
                                  various data directories is written to. By
                                  default these results are written to the
                                  screen (stdout).

   Advanced qualifiers:
   -reject             select     This specifies the names of the
                                  sub-directories of the EMBOSS data directory
                                  that should be ignored when displaying data
                                  directories.

   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
   -filename This specifies the name of the file that should be fetched
   into the current directory or searched for in all of the directories
   that EMBOSS programs search when looking for a data file. The name of
   the file is not altered when it is fetched. Any string is accepted An
   empty string is accepted
   Optional qualifiers Allowed values Default
   -showall Show all potential EMBOSS data files Yes/No No
   -fetch Fetch a data file Yes/No No
   -outf This specifies the name of the file that the results of a search
   for a file in the various data directories is written to. By default
   these results are written to the screen (stdout). Output file stdout
   Advanced qualifiers Allowed values Default
   -reject This specifies the names of the sub-directories of the EMBOSS
   data directory that should be ignored when displaying data
   directories. None
   PROSITE
   PRINTS
   CVS
   CODONS
   REBASE
   2, 3, 4
   
Input file format

   None.
   
Output file format

   All output is to stdout.
   
   When reporting the directories searched for EMBOSS data files:
----------------------------------------------------------------------
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.

.                                                            Exists
.embossdata                                                  Does not exist
/people/gwilliam                                             Exists
/people/gwilliam/.embossdata                                 Does not exist
/packages/emboss_dev/gwilliam/emboss/emboss/data             Exists
----------------------------------------------------------------------

   When reporting the datafiles found in directories:
----------------------------------------------------------------------
DIRECTORY: /packages/emboss/emboss/data

  Ebases.iub
  Eamino.dat
  Epk.dat
  Edna.melt
  Erna.melt
  EDNAFULL
  EDNAMAT
  Edayhoff.freq
  Ewhite-wimley.dat
  Eembossre.equ
  Eantigenic.dat
  Ehth.dat
  Ehth87.dat
  Esig.euk
  Esig.pro
  Epepcoil.dat
  EGC.0
  EGC.1
  EGC.2
  EGC.3
  EGC.4
  EGC.5
  EGC.6
  EBLOSUM62
  EGC.9
  EGC.10
  EGC.12
  EGC.11
  EGC.13
  EGC.14
  EGC.15
  Enakai.dat
  Eaa_acc_surface.dat
  Eaa_hydropathy.dat
  Eaa_properties.dat
  Eangles_tri.dat
  EBLOSUM30
  EBLOSUM35
  EBLOSUM40
  EBLOSUM45

etc.

DIRECTORY: /packages/emboss/emboss/data/CODONS

  Eacc.cut
  Eadenovirus5.cut
  Eadenovirus7.cut
  Eaidlav.cut
  Eanasp.cut
  Eani.cut
  Eani_h.cut
  Eanidmit.cut
  Easn.cut
  Eath.cut
  Eatu.cut
  Eavi.cut
  Ebja.cut
  Ebly.cut
  Ebme.cut


----------------------------------------------------------------------

   When reporting the location of a particular EMBOSS data file:
----------------------------------------------------------------------
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.

File ./EPAM60                                           Exists
File .embossdata/EPAM60                                 Does not exist
File /people/gwilliam/EPAM60                            Does not exist
File /people/gwilliam/.embossdata/EPAM60                Does not exist
File /packages/emboss/emboss/data/EPAM60                Exists
----------------------------------------------------------------------

Data files

   No data files are read by this program.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   When copying a file, this program will report if the file has been
   copied successfully, e.g.:
"'Epepcoil.dat' has been copied successfully."

Exit status

   It always exits with status 0
   
Known bugs

   None noted.
   
See also

   Program name                Description
   embossversion Writes the current EMBOSS version number
   
Author(s)

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

   Finished.
   
Target users

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


It should be possible to format the output for html.
