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EMBOSS: embossdata |
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.
% 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
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): -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). -showall bool Show all potential EMBOSS data files * -fetch bool Fetch a data file 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 | |
-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 |
-showall | Show all potential EMBOSS data files | Yes/No | No |
-fetch | Fetch a data file | Yes/No | No |
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 |
2, 3, 4 |
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 ----------------------------------------------------------------------
"'Epepcoil.dat' has been copied successfully."
Program name | Description |
---|---|
embossversion | Writes the current EMBOSS version number |
It should be possible to format the output for html.