| embossdata

## Function

Find and retrieve EMBOSS data files

## Description

embossdata searches for a specified data file in all the directories which can hold them and writes the results of the search to screen or (optionally) to file. Optionally, all the files in the searched directories can be displayed. Optionally, it will also copy the file from the EMBOSS standard data directory to the current directory so that you can safely edit and use it.

## Usage

Here is a sample session with embossdata

Display the directories searched for EMBOSS data files:

    % embossdata
    Find and retrieve EMBOSS data files
    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
    Find and retrieve EMBOSS data files
    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
      Emolwt.dat
      EBLOSUMN
      Eangles.dat
      tfinsect
      Efeatures.gff3protein
      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.gff2
      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
      Eresidues.iub
      Efeatures.protein
      Erna.melt
      Eamino.dat
      EBLOSUM62-12
      Eantigenic.dat
      Efeatures.gff2protein
      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/JASPAR_POLII

      dummyfile

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

      matrix_list.txt
      dummyfile
      MA0001.pfm
      MA0002.pfm
      MA0003.pfm
      MA0004.pfm
      MA0005.pfm
      MA0006.pfm
      MA0007.pfm
      MA0008.pfm
      MA0009.pfm
      MA0010.pfm
      MA0011.pfm
      MA0012.pfm
      MA0013.pfm
      MA0014.pfm
      MA0015.pfm
      MA0016.pfm
      MA0017.pfm
      MA0018.pfm
      MA0019.pfm
      MA0020.pfm
      MA0021.pfm
      MA0022.pfm
      MA0023.pfm
      MA0024.pfm
      MA0025.pfm
      MA0026.pfm
      MA0027.pfm
      MA0028.pfm
      MA0029.pfm
      MA0030.pfm
      MA0031.pfm
      MA0032.pfm
      MA0033.pfm
      MA0034.pfm
      MA0035.pfm
      MA0036.pfm
      MA0037.pfm
      MA0038.pfm
      MA0039.pfm
      MA0040.pfm
      MA0041.pfm
      MA0042.pfm
      MA0043.pfm
      MA0044.pfm
      MA0045.pfm
      MA0046.pfm
      MA0047.pfm
      MA0048.pfm
      MA0049.pfm
      MA0050.pfm
      MA0051.pfm
      MA0052.pfm
      MA0053.pfm
      MA0054.pfm
      MA0055.pfm
      MA0056.pfm
      MA0057.pfm
      MA0058.pfm
      MA0059.pfm
      MA0060.pfm
      MA0061.pfm
      MA0062.pfm
      MA0063.pfm
      MA0064.pfm
      MA0065.pfm
      MA0066.pfm
      MA0067.pfm
      MA0068.pfm
      MA0069.pfm
      MA0070.pfm
      MA0071.pfm
      MA0072.pfm
      MA0073.pfm
      MA0074.pfm
      MA0075.pfm
      MA0076.pfm
      MA0077.pfm
      MA0078.pfm
      MA0079.pfm
      MA0080.pfm
      MA0081.pfm
      MA0082.pfm
      MA0083.pfm
      MA0084.pfm
      MA0085.pfm
      MA0086.pfm
      MA0087.pfm
      MA0088.pfm
      MA0089.pfm
      MA0090.pfm
      MA0091.pfm
      MA0092.pfm
      MA0093.pfm
      MA0094.pfm
      MA0095.pfm
      MA0096.pfm
      MA0097.pfm
      MA0098.pfm
      MA0099.pfm
      MA0100.pfm
      MA0101.pfm
      MA0102.pfm
      MA0103.pfm
      MA0104.pfm
      MA0105.pfm
      MA0106.pfm
      MA0107.pfm
      MA0108.pfm
      MA0109.pfm
      MA0110.pfm
      MA0111.pfm
      MA0112.pfm
      MA0113.pfm
      MA0114.pfm
      MA0115.pfm
      MA0116.pfm
      MA0117.pfm
      MA0118.pfm
      MA0119.pfm
      MA0120.pfm
      MA0121.pfm
      MA0122.pfm
      MA0123.pfm

    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/JASPAR_CNE

      dummyfile

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

      MF0001.pfm
      MF0002.pfm
      MF0003.pfm
      MF0004.pfm
      MF0005.pfm
      MF0006.pfm
      MF0007.pfm
      MF0008.pfm
      MF0009.pfm
      MF0010.pfm
      MF0011.pfm
      matrix_list.txt
      dummyfile

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

      PF0001.pfm
      PF0002.pfm
      PF0003.pfm
      PF0004.pfm
      PF0005.pfm
      PF0006.pfm
      PF0007.pfm
      PF0008.pfm
      PF0009.pfm
      PF0010.pfm
      PF0011.pfm
      PF0012.pfm
      PF0013.pfm
      PF0014.pfm
      PF0015.pfm
      PF0016.pfm
      PF0017.pfm
      PF0018.pfm
      PF0019.pfm
      PF0020.pfm
      PF0021.pfm
      PF0022.pfm
      PF0023.pfm
      PF0024.pfm
      PF0025.pfm
      PF0026.pfm
      PF0027.pfm
      PF0028.pfm
      PF0029.pfm
      PF0030.pfm
      PF0031.pfm
      PF0032.pfm
      PF0033.pfm
      PF0034.pfm
      PF0035.pfm
      PF0036.pfm
      PF0037.pfm
      PF0038.pfm
      PF0039.pfm
      PF0040.pfm
      PF0041.pfm
      PF0042.pfm
      PF0043.pfm
      PF0044.pfm
      PF0045.pfm
      PF0046.pfm
      PF0047.pfm
      PF0048.pfm
      PF0049.pfm
      PF0050.pfm
      PF0051.pfm
      PF0052.pfm
      PF0053.pfm
      PF0054.pfm
      PF0055.pfm
      PF0056.pfm
      PF0057.pfm
      PF0058.pfm
      PF0059.pfm
      PF0060.pfm
      PF0061.pfm
      PF0062.pfm
      PF0063.pfm
      PF0064.pfm
      PF0065.pfm
      PF0066.pfm
      PF0067.pfm
      PF0068.pfm
      PF0069.pfm
      PF0070.pfm
      PF0071.pfm
      PF0072.pfm
      PF0073.pfm
      PF0074.pfm
      PF0075.pfm
      PF0076.pfm
      PF0077.pfm
      PF0078.pfm
      PF0079.pfm
      PF0080.pfm
      PF0081.pfm
      PF0082.pfm
      PF0083.pfm
      PF0084.pfm
      PF0085.pfm
      PF0086.pfm
      PF0087.pfm
      PF0088.pfm
      PF0089.pfm
      PF0090.pfm
      PF0091.pfm
      PF0092.pfm
      PF0093.pfm
      PF0094.pfm
      PF0095.pfm
      PF0096.pfm
      PF0097.pfm
      PF0098.pfm
      PF0099.pfm
      PF0100.pfm
      PF0101.pfm
      PF0102.pfm
      PF0103.pfm
      PF0104.pfm
      PF0105.pfm
      PF0106.pfm
      PF0107.pfm
      PF0108.pfm
      PF0109.pfm
      PF0110.pfm
      PF0111.pfm
      PF0112.pfm
      PF0113.pfm
      PF0114.pfm
      PF0115.pfm
      PF0116.pfm
      PF0117.pfm
      PF0118.pfm
      PF0119.pfm
      PF0120.pfm
      PF0121.pfm
      PF0122.pfm
      PF0123.pfm
      PF0124.pfm
      PF0125.pfm
      PF0126.pfm
      PF0127.pfm
      PF0128.pfm
      PF0129.pfm
      PF0130.pfm
      PF0131.pfm
      PF0132.pfm
      PF0133.pfm
      PF0134.pfm
      PF0135.pfm
      PF0136.pfm
      PF0137.pfm
      PF0138.pfm
      PF0139.pfm
      PF0140.pfm
      PF0141.pfm
      PF0142.pfm
      PF0143.pfm
      PF0144.pfm
      PF0145.pfm
      PF0146.pfm
      PF0147.pfm
      PF0148.pfm
      PF0149.pfm
      PF0150.pfm
      PF0151.pfm
      PF0152.pfm
      PF0153.pfm
      PF0154.pfm
      PF0155.pfm
      PF0156.pfm
      PF0157.pfm
      PF0158.pfm
      PF0159.pfm
      PF0160.pfm
      PF0161.pfm
      PF0162.pfm
      PF0163.pfm
      PF0164.pfm
      PF0165.pfm
      PF0166.pfm
      PF0167.pfm
      PF0168.pfm
      PF0169.pfm
      PF0170.pfm
      PF0171.pfm
      PF0172.pfm
      PF0173.pfm
      PF0174.pfm
      matrix_list.txt
      dummyfile

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

      dummyfile

    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
    Find and retrieve EMBOSS data files

    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
    Find and retrieve 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.

    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 first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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

Many EMBOSS programs use a data file. The data files are typically kept in a standard directory in the EMBOSS installation (`.../emboss/emboss/data/`). When an EMBOSS programs require a data file, it search for it in the following order of directories:

- The current directory
- `.embossdata` subdirectory in the current directory
- Your home directory
- `.embossdata` subdirectory in your home directory
- The EMBOSS standard data directory

EMBOSS will use the data file it finds first from the above directories. For example, a data file in the current directory is used in preference to a file of the same name in the EMBOSS standard data directory.

It is sometimes necessary to modify a data file to change the behaviour of an EMBOSS program. To do this safely, you should copy the data file from the EMBOSS standard data directory to one of the other directories, such as the current directory or your home directory, before editing it. embossdata helps here by displaying the names of data files in all the directories which could hold them, and copying a data file from the EMBOSS standard data directory to the current directory.

By convention, all EMBOSS data file names start with the character 'E', to distinguish them from other files on your system. For example genetic codes to translate codons to amino acids are held in data files called "EGC.0", "EGC.1", "EGC.2", etc.

### -filename option

Name of data file to search for or copy into the current directory from the EMBOSS standard data directory. The name of the file is not altered when it is fetched. (Any string is accepted).

### -outfile option

Name of file containing the results of searching the data directories. By default this is written to the screen (`stdout`).

### -reject option

The names of sub-directories of the EMBOSS data directory that should be ignored when displaying data directories.

## 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 to a file

## 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.