| 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

Here is a sample session with embossdata

Display the directories searched for EMBOSS data files:

    % embossdata
    Finds or fetches the data files read in by the 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.

    .                                                            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 the data files read in by the EMBOSS programs

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

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

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

      dummyfile
      andn920101
      argp820101
      argp820102
      argp820103
      begf750101
      begf750102
      begf750103
      bhar880101
      bigc670101
      biov880101
      biov880102
      broc820101
      broc820102
      bulh740101
      bulh740102
      buna790101
      buna790102
      buna790103
      bura740101
      bura740102
      cham810101
      cham820101
      cham820102
      cham830101
      cham830102
      cham830103
      cham830104
      cham830105
      cham830106
      cham830107
      cham830108
      choc750101
      choc760101
      choc760102
      choc760103
      choc760104
      chop780101
      chop780201
      chop780202
      chop780203
      chop780204
      chop780205
      chop780206
      chop780207
      chop780208
      chop780209
      chop780210
      chop780211
      chop780212
      chop780213
      chop780214
      chop780215
      chop780216
      cidh920101
      cidh920102
      cidh920103
      cidh920104
      cidh920105
      cohe430101
      craj730101
      craj730102
      craj730103
      dawd720101
      daym780101
      daym780201
      desm900101
      desm900102
      eisd840101
      eisd860101
      eisd860102
      eisd860103
      fasg760101
      fasg760102
      fasg760103
      fasg760104
      fasg760105
      fauj830101
      fauj880101
      fauj880102
      fauj880103
      fauj880104
      fauj880105
      fauj880106
      fauj880107
      fauj880108
      fauj880109
      fauj880110
      fauj880111
      fauj880112
      fauj880113
      fina770101
      fina910101
      fina910102
      fina910103
      fina910104
      garj730101
      geim800101
      geim800102
      geim800103
      geim800104
      geim800105
      geim800106
      geim800107
      geim800108
      geim800109
      geim800110
      geim800111
      gold730101
      gold730102
      grar740101
      grar740102
      grar740103
      guyh850101
      hopa770101
      hopt810101
      hutj700101
      hutj700102
      hutj700103
      isoy800101
      isoy800102
      isoy800103
      isoy800104
      isoy800105
      isoy800106
      isoy800107
      isoy800108
      janj780101
      janj780102
      janj780103
      janj790101
      janj790102
      jond750101
      jond750102
      jond920101
      jond920102
      jukt750101
      junj780101
      kanm800101
      kanm800102
      kanm800103
      kanm800104
      karp850101
      karp850102
      karp850103
      khag800101
      klep840101
      kriw710101
      kriw790101
      kriw790102
      kriw790103
      kytj820101
      lawe840101
      levm760101
      levm760102
      levm760103
      levm760104
      levm760105
      levm760106
      levm760107
      levm780101
      levm780102
      levm780103
      levm780104
      levm780105
      levm780106
      lewp710101
      lifs790101
      lifs790102
      lifs790103
      manp780101
      maxf760101
      maxf760102
      maxf760103
      maxf760104
      maxf760105
      maxf760106
      mcmt640101
      meej800101
      meej800102
      meej810101
      meej810102
      meih800101
      meih800102
      meih800103
      miys850101
      nagk730101
      nagk730102
      nagk730103
      nakh900101
      nakh900102
      nakh900103
      nakh900104
      nakh900105
      nakh900106
      nakh900107
      nakh900108
      nakh900109
      nakh900110
      nakh900111
      nakh900112
      nakh900113
      nakh920101
      nakh920102
      nakh920103
      nakh920104
      nakh920105
      nakh920106
      nakh920107
      nakh920108
      nisk800101
      nisk860101
      nozy710101
      oobm770101
      oobm770102
      oobm770103
      oobm770104
      oobm770105
      oobm850101
      oobm850102
      oobm850103
      oobm850104
      oobm850105
      palj810101
      palj810102
      palj810103
      palj810104
      palj810105
      palj810106
      palj810107
      palj810108
      palj810109
      palj810110
      palj810111
      palj810112
      palj810113
      palj810114
      palj810115
      palj810116
      parj860101
      pliv810101
      ponp800101
      ponp800102
      ponp800103
      ponp800104
      ponp800105
      ponp800106
      ponp800107
      ponp800108
      pram820101
      pram820102
      pram820103
      pram900101
      pram900102
      pram900103
      pram900104
      ptio830101
      ptio830102
      qian880101
      qian880102
      qian880103
      qian880104
      qian880105
      qian880106
      qian880107
      qian880108
      qian880109
      qian880110
      qian880111
      qian880112
      qian880113
      qian880114
      qian880115
      qian880116
      qian880117
      qian880118
      qian880119
      qian880120
      qian880121
      qian880122
      qian880123
      qian880124
      qian880125
      qian880126
      qian880127
      qian880128
      qian880129
      qian880130
      qian880131
      qian880132
      qian880133
      qian880134
      qian880135
      qian880136
      qian880137
      qian880138
      qian880139
      racs770101
      racs770102
      racs770103
      racs820101
      racs820102
      racs820103
      racs820104
      racs820105
      racs820106
      racs820107
      racs820108
      racs820109
      racs820110
      racs820111
      racs820112
      racs820113
      racs820114
      rada880101
      rada880102
      rada880103
      rada880104
      rada880105
      rada880106
      rada880107
      rada880108
      ricj880101
      ricj880102
      ricj880103
      ricj880104
      ricj880105
      ricj880106
      ricj880107
      ricj880108
      ricj880109
      ricj880110
      ricj880111
      ricj880112
      ricj880113
      ricj880114
      ricj880115
      ricj880116
      ricj880117
      robb760101
      robb760102
      robb760103
      robb760104
      robb760105
      robb760106
      robb760107
      robb760108
      robb760109
      robb760110
      robb760111
      robb760112
      robb760113
      robb790101
      rosg850101
      rosg850102
      rosm880101
      rosm880102
      rosm880103
      simz760101
      snep660101
      snep660102
      snep660103
      snep660104
      suem840101
      suem840102
      swer830101
      tans770101
      tans770102
      tans770103
      tans770104
      tans770105
      tans770106
      tans770107
      tans770108
      tans770109
      tans770110
      vasm830101
      vasm830102
      vasm830103
      velv850101
      vent840101
      vheg790101
      warp780101
      weba780101
      werd780101
      werd780102
      werd780103
      werd780104
      woec730101
      wolr810101
      wols870101
      wols870102
      wols870103
      yutk870101
      yutk870102
      yutk870103
      yutk870104
      zasb820101
      zimj680101
      zimj680102
      zimj680103
      zimj680104
      zimj680105
      aurr980101
      aurr980102
      aurr980103
      aurr980104
      aurr980105
      aurr980106
      aurr980107
      aurr980108
      aurr980109
      aurr980110
      aurr980111
      aurr980112
      aurr980113
      aurr980114
      aurr980115
      aurr980116
      aurr980117
      aurr980118
      aurr980119
      aurr980120
      onek900101
      onek900102
      vinm940101
      vinm940102
      vinm940103
      vinm940104
      munv940101
      munv940102
      munv940103
      munv940104
      munv940105
      wimw960101
      kimc930101
      monm990101
      blam930101
      pars000101
      pars000102
      kums000101
      kums000102
      kums000103
      kums000104
      takk010101
      fodm020101
      nadh010101
      nadh010102
      nadh010103
      nadh010104
      nadh010105
      nadh010106
      nadh010107
      monm990201
      koep990101
      koep990102
      cedj970101
      cedj970102
      cedj970103
      cedj970104
      cedj970105
      fuks010101
      fuks010102
      fuks010103
      fuks010104
      fuks010105
      fuks010106
      fuks010107
      fuks010108
      fuks010109
      fuks010110
      fuks010111
      fuks010112
      avbf000101
      avbf000102
      avbf000103
      avbf000104
      avbf000105
      avbf000106
      avbf000107
      avbf000108
      avbf000109
      yanj020101
      mits020101
      tsaj990101
      tsaj990102
      cosi940101
      ponp930101
      wilm950101
      wilm950102
      wilm950103
      wilm950104
      kuhl950101
      guod860101
      jurd980101

    DIRECTORY: /homes/pmr/local/share/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
      Ebmo.cut
      Ebna.cut
      Ebov.cut
      Ebovsp.cut
      Ebst.cut
      Ebsu.cut
      Ebsu_h.cut
      Ecac.cut
      Ecal.cut
      Eccr.cut
      Ecel.cut
      Echi.cut
      Echicken.cut
      Echisp.cut
      Echk.cut
      Echmp.cut
      Echnt.cut
      Echos.cut
      Echzm.cut
      Echzmrubp.cut
      Ecpx.cut
      Ecre.cut
      Ecrisp.cut
      Ectr.cut
      Edayhoff.cut
      Eddi.cut
      Eddi_h.cut
      Edog.cut
      Edro.cut
      Edro_h.cut
      Edrosophila.cut
      Eeca.cut
      Eeco.cut
      Eeco_h.cut
      Eecoli.cut
      Ef1.cut
      Efish.cut
      Efmdvpolyp.cut
      Eham.cut
      Ehha.cut
      Ehin.cut
      Ehma.cut
      Ehum.cut
      Ehuman.cut
      Ekla.cut
      Ekpn.cut
      Ella.cut
      Emac.cut
      Emaize.cut
      Emam_h.cut
      Emixlg.cut
      Emouse.cut
      Emsa.cut
      Emse.cut
      Emta.cut
      Emtu.cut
      Emus.cut
      Emussp.cut
      Emva.cut
      Emze.cut
      Emzecp.cut
      Encr.cut
      Eneu.cut
      Engo.cut
      Eoncsp.cut
      Epae.cut
      Epea.cut
      Epet.cut
      Epfa.cut
      Ephix174.cut
      Ephv.cut
      Ephy.cut
      Epig.cut
      Epolyomaa2.cut
      Epombe.cut
      Epombecai.cut
      Epot.cut
      Eppu.cut
      Epse.cut
      Epsy.cut
      Epvu.cut
      Erab.cut
      Erabbit.cut
      Erabsp.cut
      Erat.cut
      Eratsp.cut
      Erca.cut
      Erhm.cut
      Eric.cut
      Erle.cut
      Erme.cut
      Ersp.cut
      Esalsp.cut
      Esau.cut
      Esco.cut
      Esgi.cut
      Eshp.cut
      Eshpsp.cut
      Esli.cut
      Eslm.cut
      Esma.cut
      Esmi.cut
      Esmu.cut
      Esoy.cut
      Espi.cut
      Espn.cut
      Espo.cut
      Espo_h.cut
      Espu.cut
      Esta.cut
      Esty.cut
      Esus.cut
      Esv40.cut
      Esyhsp.cut
      Esynsp.cut
      Etbr.cut
      Etcr.cut
      Eter.cut
      Etetsp.cut
      Etob.cut
      Etobcp.cut
      Etom.cut
      Etrb.cut
      Evco.cut
      Ewht.cut
      Exel.cut
      Exenopus.cut
      Eyeast.cut
      Eyeastcai.cut
      Eyen.cut
      Eysc.cut
      Eysc_h.cut
      Eyscmt.cut
      Eysp.cut
      Ezebrafish.cut
      Ezma.cut
      EAedes_atropalpus.cut
      EDictyostelium_discoideum.cut
      EAndroctonus_australis.cut
      EAmblyomma_americanum.cut
      EAedes_albopictus.cut
      EAedes_aegypti.cut
      EAphrodite_aculeata.cut
      EAsellus_aquaticus.cut
      EAcanthocheilonema_viteae.cut
      EAstacus_astacus.cut
      EAgelenopsis_aperta.cut
      EAcrolepiopsis_assectella.cut
      EAnadara_trapezia.cut

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

      dummyfile
      embossre.enz
      embossre.ref
      embossre.sup

Example 3

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

    % embossdata -fetch -filename Epepcoil.dat
    Finds or fetches the data files read in by the 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 -filename EPAM60
    Finds or fetches the data files read in by the 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 (* 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.

       Additional (Optional) qualifiers (* if not always prompted):
       -showall            toggle     Show all potential EMBOSS data files
    *  -fetch              boolean    Fetch a data file
       -outfile            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 (Unprompted) qualifiers:
       -reject             selection  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 deaths

Standard (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
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.