EMBOSS: embossdata

| embossdata

## Function

Finds or fetches data files read by 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

Here is a sample session with embossdata

Display the directories searched for EMBOSS data files:

    % embossdata
    Finds or fetches data files read by EMBOSS programs
    Data file name:

    # 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
    /homes/pmr                                                   Exists
    /homes/pmr/.embossdata                                       Does not exist
    /homes/pmr/local/share/EMBOSS/data/                          Exists

Example 2

Display the names of data files in all of the possible data directories: This is run on a small test system and so the results will probably be different when you run this.

    % embossdata -showall
    Finds or fetches data files read by EMBOSS programs
    Data file name:

    DIRECTORY: /homes/pmr/local/share/EMBOSS/data/

      EGC.10
      EGC.11
      EGC.12
      EGC.13
      EGC.14
      EGC.15
      EGC.16
      EGC.21
      EGC.22
      EGC.23
      EPAM10
      EPAM20
      EPAM30
      EPAM40
      EPAM50
      EPAM60
      EPAM70
      EPAM80
      EPAM90
      edialignmat
      Eenergy.dat
      EDNAMAT
      Etags.swiss
      Matrices.proteinstructure
      Emass.dat
      Etags.gffprotein
      EGC.txt
      Ehth87.dat
      Eaa_hydropathy.dat
      Enakai.dat
      EGC.0
      EGC.1
      EGC.2
      EGC.3
      EGC.4
      EGC.5
      EGC.6
      EGC.9
      Eangles_tri.dat
      Epprofile
      Efreqs.dat
      Emwfilter.dat
      ENUC.4.2
      ENUC.4.4
      Etags.embl
      Etags.gff3
      tp400_trans
      Etags.gff
      Etags.pir
      EPAM100
      EPAM110
      EPAM120
      EPAM130
      EPAM140
      EPAM150
      EPAM160
      EPAM170
      EPAM180
      EPAM190
      EPAM200
      EPAM210
      EPAM220
      EPAM230
      EPAM240
      EPAM250
      EPAM260
      EPAM270
      EPAM280
      EPAM290
      EPAM300
      EPAM310
      EPAM320
      EPAM330
      EPAM340
      EPAM350
      EPAM360
      EPAM370
      EPAM380
      EPAM390
      EPAM400
      EPAM410
      EPAM420
      EPAM430
      EPAM440
      EPAM450
      EPAM460
      EPAM470
      EPAM480
      EPAM490
      EPAM500
      Ehet.dat
      Evdw.dat
      Edna.melt
      Eaa_properties.dat
      Eamino.dat~
      EBLOSUMN
      Eangles.dat
      tfinsect
      tffungi
      Etcode.dat
      tfother
      tfplant
      Ehth.dat
      Etags.emboss
      tp400_dna
      Ebases.iub
      Efeatures.gff
      Efeatures.pir
      Etags.protein
      Eaa_acc_surface.dat
      Epepcoil.dat
      Ememe.dat
      Efeatures.gffprotein
      Eprior1.plib
      Efeatures.embl
      Efeatures.gff3
      EBLOSUM30
      EBLOSUM35
      EBLOSUM40
      EBLOSUM45
      EBLOSUM50
      EBLOSUM55
      EBLOSUM60
      EBLOSUM62
      EBLOSUM65
      EBLOSUM70
      EBLOSUM75
      EBLOSUM80
      EBLOSUM85
      EBLOSUM90
      EDNAFULL
      Emassmod.dat
      Efeatures.emboss
      Matrices.nucleotide
      Epk.dat
      tfvertebrate
      Efeatures.protein
      Erna.melt
      Eamino.dat
      EBLOSUM62-12
      Eantigenic.dat
      Efeatures.swiss
      Eembl.ior
      tp400_prot
      Eprior30.plib
      Esig.euk
      Esig.pro
      EGC.index
      Ewhite-wimley.dat
      Matrices.protein
      embossre.equ
      Edayhoff.freq

    DIRECTORY: /homes/pmr/local/share/EMBOSS/data/REBASE

      dummyfile
      embossre.enz
      embossre.equ
      embossre.ref
      embossre.sup

    DIRECTORY: /homes/pmr/local/share/EMBOSS/data/AAINDEX

      dummyfile
      kytj820101
      chop780101
      chop780201
      chop780202
      chop780203
      chop780204
      chop780205
      chop780206
      chop780207
      chop780208
      chop780209
      chop780210
      chop780211
      chop780212
      chop780213
      chop780214
      chop780215
      chop780216

    DIRECTORY: /homes/pmr/local/share/EMBOSS/data/CODONS

      EAedes_aegypti.cut
      Ecyapa.cut
      Eerwct.cut
      Ehuman.cut
      Eratsp.cut
      Esta.cut
      Ecaeel.cut
      EAedes_atropalpus.cut
      Estaau.cut
      Edrome_high.cut
      Echmp.cut
      Eyerpe.cut
      Ecrisp.cut
      Efish.cut
      Esty.cut
      Ehalsa.cut
      Emyctu.cut
      Esus.cut
      Echnt.cut
      Edicdi.cut
      Echos.cut
      EAmblyomma_americanum.cut
      Encr.cut
      Epolyomaa2.cut
      EAphrodite_aculeata.cut
      Ebommo.cut
      Eysc_h.cut
      Eschpo_high.cut
      Etob.cut
      Eneu.cut
      Etom.cut
      Ephix174.cut
      Emedsa.cut
      Eanidmit.cut
      Emsa.cut
      Engo.cut
      Emse.cut
      Epethy.cut
      Esynsp.cut
      Emta.cut
      Etrb.cut
      Eani_h.cut
      Etheth.cut
      Echicken.cut
      Emtu.cut
      Emva.cut
      Ebpphx.cut
      Eschpo_cai.cut
      Emus.cut
      Eacc.cut
      Eorysa.cut
      Eham.cut
      Ebraja.cut
      Eshpsp.cut
      Emanse.cut
      Emaize_chl.cut
      Edro_h.cut
      Echzm.cut
      Echzmrubp.cut
      Emze.cut
      Evibch.cut
      Epombecai.cut
      EAstacus_astacus.cut
      Ebrana.cut
      Erhoca.cut
      Eemeni_high.cut
      Evco.cut
      Ehha.cut
      Eanasp.cut
      Ebacme.cut
      Esyhsp.cut
      Erabit.cut
      Eneigo.cut
      Ecanal.cut
      Ehin.cut
      Elyces.cut
      Eklepn.cut
      Ebrare.cut
      Eyscmt.cut
      Epseae.cut
      Eemeni_mit.cut
      Ehma.cut
      Eani.cut
      Ecanfa.cut
      Emixlg.cut
      Ecaucr.cut
      Epae.cut
      Ephavu.cut
      Ebovin.cut
      Ehorvu.cut
      Ebacst.cut
      Ebacsu.cut
      Echlre.cut
      Epea.cut
      Edrome.cut
      Esheep.cut
      Erabsp.cut
      Epfa.cut
      Esalsa.cut
      Easn.cut
      Ebacsu_high.cut
      Eecoli_high.cut
      Eath.cut
      Epet.cut
      Ebja.cut
      Emacfa.cut
      EAcanthocheilonema_viteae.cut
      Esalsp.cut
      Eyeast_cai.cut
      Eatu.cut
      Echltr.cut
      Eoncmy.cut
      Eavi.cut
      Ecac.cut
      Eemeni.cut
      Esalty.cut
      Ehum.cut
      Eprovu.cut
      Epig.cut
      Esoybn.cut
      Ecal.cut
      Ephv.cut
      Ephy.cut
      Ebme.cut
      Erhosh.cut
      Ebna.cut
      Ewht.cut
      Ebly.cut
      Ebmo.cut
      Ef1.cut
      Emetth.cut
      EAnadara_trapezia.cut
      Ebovsp.cut
      Eccr.cut
      Erhile.cut
      Eplafa.cut
      Erhime.cut
      Ebov.cut
      Ecel.cut
      Eoncsp.cut
      Epsepu.cut
      Estrco.cut
      Echi.cut
      Epot.cut
      Echk.cut
      Epsesm.cut
      Etetsp.cut
      Eklula.cut
      Etetth.cut
      Ebsu_h.cut
      Ebst.cut
      Ebsu.cut
      Emaize.cut
      Eppu.cut
      Exel.cut
      Emouse.cut
      Eagrtu.cut
      Epse.cut
      Eserma.cut
      Eazovi.cut
      Epsy.cut
      Ewheat.cut
      Eyeast.cut
      Eacica.cut
      Erab.cut
      Eddi.cut
      EAedes_albopictus.cut
      Espo_h.cut
      Epvu.cut
      Etobac.cut
      Erat.cut
      Erca.cut
      Eaidlav.cut
      Ezebrafish.cut
      Ecpx.cut
      Ecre.cut
      Cut.index
      Estrmu.cut
      Efmdvpolyp.cut
      Etobcp.cut
      Eyeastcai.cut
      Estrpn.cut
      Eyen.cut
      Ectr.cut
      Estrpu.cut
      Emzecp.cut
      Exenopus.cut
      Edrosophila.cut
      Eeco_h.cut
      Eorysa_chl.cut
      Erhm.cut
      Eric.cut
      Ekla.cut
      Earath.cut
      Eeca.cut
      Echick.cut
      EAedes.cut
      Eeco.cut
      Erle.cut
      Edog.cut
      Emam_h.cut
      Eyeast_high.cut
      Erme.cut
      Esau.cut
      Esoltu.cut
      Emammal_high.cut
      Esco.cut
      Ekpn.cut
      Edro.cut
      Eadenovirus5.cut
      Exenla.cut
      Eadenovirus7.cut
      Etobac_chl.cut
      Elacdl.cut
      Esgi.cut
      EDictyostelium_discoideum.cut
      Erabbit.cut
      Eddi_h.cut
      Eshp.cut
      Ersp.cut
      Eysc.cut
      Ella.cut
      Ecrigr.cut
      Emac.cut
      Emarpo_chl.cut
      Eecoli.cut
      Edicdi_high.cut
      Eysp.cut
      Esv40.cut
      Eyeren.cut
      Edayhoff.cut
      Etrybr.cut
      Ehaein.cut
      Etrycr.cut
      Esli.cut
      Esynco.cut
      Esma.cut
      Eslm.cut
      Eschma.cut
      Esmi.cut
      Esyncy.cut
      Ezma.cut
      Etbr.cut
      Esmu.cut
      Etcr.cut
      Ehalma.cut
      Eneucr.cut
      Echisp.cut
      Espi.cut
      Emussp.cut
      Ecloab.cut
      Epombe.cut
      Espiol.cut
      Esoy.cut
      Espn.cut
      Espo.cut
      Eter.cut
      Eyeast_mit.cut
      Eschpo.cut
      Espu.cut

Example 3

Make a copy of an EMBOSS data file in the current directory:

    % embossdata -fetch Epepcoil.dat
    Finds or fetches data files read by EMBOSS programs

    File '/homes/pmr/local/share/EMBOSS/data/Epepcoil.dat' has been copied successfully.

Go to the output files for this example

Example 4

Display the directories which contain a particular EMBOSS data file:

    % embossdata EPAM60
    Finds or fetches data files read by EMBOSS programs

    # 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                                                     Does not exist
    File .embossdata/EPAM60                                           Does not exist
    File /homes/pmr/EPAM60                                            Does not exist
    File /homes/pmr/.embossdata/EPAM60                                Does not exist
    File /homes/pmr/local/share/EMBOSS/data/EPAM60                    Exists

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-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. (Any string is
                                      accepted)

       Additional (Optional) qualifiers (* if not always prompted):
       -showall            toggle     Show all potential EMBOSS data files
    *  -fetch              boolean    Fetch a data file
       -outfile            outfile    [stdout] 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 (Unprompted) qualifiers:
       -reject             selection  [3, 5, 6] This specifies the names of the
                                      sub-directories of the EMBOSS data directory
                                      that should be ignored when displaying data
                                      directories.

       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 dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-filename] (Parameter 1) | 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
Additional (Optional) qualifiers | Allowed values | Default
-showall | Show all potential EMBOSS data files | Toggle value Yes/No | No
-fetch | Fetch a data file | Boolean value Yes/No | No
-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). | Output file | stdout
Advanced (Unprompted) 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. | Choose from selection list of values | 3, 5, 6

## Input file format

None.

## Output file format

All output is to stdout by default.

### Output files for usage example 3

### File: Epepcoil.dat

    # Input data for PEPCOIL
    # from Lupas A, van Dyke M & Stock J; Science 252:1162-4 (1991)
    #
    #   Freq in       Relative occurrence at heptad position
    # R GenBank     a      b      c      d      e      f      g
      L  9.33     3.167  0.297  0.398  3.902  0.585  0.501  0.483
      I  5.35     2.597  0.098  0.345  0.894  0.514  0.471  0.431
      V  6.42     1.665  0.403  0.386  0.949  0.211  0.342  0.360
      M  2.34     2.240  0.370  0.480  1.409  0.541  0.772  0.663
      F  3.88     0.531  0.076  0.403  0.662  0.189  0.106  0.013
      Y  3.16     1.417  0.090  0.122  1.659  0.190  0.130  0.155
      G  7.10     0.045  0.275  0.578  0.216  0.211  0.426  0.156
      A  7.59     1.297  1.551  1.084  2.612  0.377  1.248  0.877
      K  5.72     1.375  2.639  1.763  0.191  1.815  1.961  2.795
      R  5.39     0.659  1.163  1.210  0.031  1.358  1.937  1.798
      H  2.25     0.347  0.275  0.679  0.395  0.294  0.579  0.213
      E  6.10     0.262  3.496  3.108  0.998  5.685  2.494  3.048
      D  5.03     0.030  2.352  2.268  0.237  0.663  1.620  1.448
      Q  4.27     0.179  2.114  1.778  0.631  2.550  1.578  2.526
      N  4.25     0.835  1.475  1.534  0.039  1.722  2.456  2.280
      S  7.28     0.382  0.583  1.052  0.419  0.525  0.916  0.628
      T  5.97     0.169  0.702  0.955  0.654  0.791  0.843  0.647
      C  1.86     0.824  0.022  0.308  0.152  0.180  0.156  0.044
      W  1.41     0.240  0.0    0.0    0.456  0.019  0.0    0.0
      P  5.28     0.0    0.008  0.0    0.013  0.0    0.0    0.0

## 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)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

## 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.