EMBOSS: embossdata

| ## 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.