embossdata

Function

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:

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

Command line arguments


Input file format

None.

Output file format

All output is to stdout by default.

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.

Author(s)

History

Target users

Comments