EMBOSS: embossdata

| embossdata

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## 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/user                                                   Exists
    /homes/user/.embossdata                                       Exists
    /homes/user/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/user/local/share/EMBOSS/data/

      DRCAT.dat
      EBLOSUM30
      EBLOSUM35
      EBLOSUM40
      EBLOSUM45
      EBLOSUM50
      EBLOSUM55
      EBLOSUM60
      EBLOSUM62
      EBLOSUM62-12
      EBLOSUM65
      EBLOSUM70
      EBLOSUM75
      EBLOSUM80
      EBLOSUM85
      EBLOSUM90
      EBLOSUMN
      EDAM.obo
      EDNAFULL
      EDNAMAT
      EDNASIMPLE
      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
      EGC.index
      EGC.txt
      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.gff2
      Efeatures.gff2protein
      Efeatures.gff3
      Efeatures.gff3protein
      Efeatures.pir
      Efeatures.protein
      Efeatures.refseqp
      Efeatures.swiss
      Efreqs.dat
      Ehet.dat
      Ehth.dat
      Ehth87.dat
      Emass.dat
      Emassmod.dat
      Ememe.dat
      Emethylsites.dat
      Emolwt.dat
      Emwfilter.dat
      Enakai.dat
      EnsemblAliases.dat
      EnsemblIdentifiers.dat
      Epepcoil.dat
      Epk.dat
      Epprofile
      Eprior1.plib
      Eprior30.plib
      Eresidues.iub
      Erna.melt
      Esig.euk
      Esig.pro
      Etags.embl
      Etags.emboss
      Etags.gff2
      Etags.gff2protein
      Etags.gff3
      Etags.gff3protein
      Etags.pir
      Etags.protein
      Etags.refseqp
      Etags.swiss
      Etcode.dat
      Evdw.dat
      Ewhite-wimley.dat
      Matrices.nucleotide
      Matrices.protein
      Matrices.proteinstructure
      SSSUB
      edialignmat
      tffungi
      tfinsect
      tfother
      tfplant
      tfvertebrate
      tp400_dna
      tp400_prot
      tp400_trans

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

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

    DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM_HOMEO

      dummyfile
      matrix_list.txt

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

      dummyfile
      matrix_list.txt

    DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_CNE

      dummyfile
      matrix_list.txt

    DIRECTORY: /homes/user/local/share/EMBOSS/data/TAXONOMY

      division.dmp
      gencode.dmp
      merged.dmp
      names.dmp
      nodes.dmp

    DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM_HLH

      dummyfile
      matrix_list.txt

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

      dummyfile
      matrix_list.txt

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

      dummyfile
      matrix_list.txt

    DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM

      dummyfile
      matrix_list.txt

    DIRECTORY: /homes/user/local/share/EMBOSS/data/OBO

      chebi.obo
      eco.obo
      evidence_code.obo
      gene_ontology.1_2.obo
      pathway.obo
      ro.obo
      so.obo
      software.obo

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

      MA0070.1.pfm
      MA0071.1.pfm
      MA0072.1.pfm
      MA0073.1.pfm
      MA0074.1.pfm
      MA0075.1.pfm
      MA0076.1.pfm
      MA0077.1.pfm
      MA0078.1.pfm
      MA0079.1.pfm
      MA0079.2.pfm
      dummyfile
      matrix_list.txt

    DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_POLII

      dummyfile
      matrix_list.txt

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

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

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

      Cut.index
      EAcanthocheilonema_viteae.cut
      EAedes.cut
      EAedes_aegypti.cut
      EAedes_albopictus.cut
      EAedes_atropalpus.cut
      EAmblyomma_americanum.cut
      EAnadara_trapezia.cut
      EAphrodite_aculeata.cut
      EAstacus_astacus.cut
      EDictyostelium_discoideum.cut
      Eacc.cut
      Eacica.cut
      Eadenovirus5.cut
      Eadenovirus7.cut
      Eagrtu.cut
      Eaidlav.cut
      Eanasp.cut
      Eani.cut
      Eani_h.cut
      Eanidmit.cut
      Earath.cut
      Easn.cut
      Eath.cut
      Eatu.cut
      Eavi.cut
      Eazovi.cut
      Ebacme.cut
      Ebacst.cut
      Ebacsu.cut
      Ebacsu_high.cut
      Ebja.cut
      Ebly.cut
      Ebme.cut
      Ebmo.cut
      Ebna.cut
      Ebommo.cut
      Ebov.cut
      Ebovin.cut
      Ebovsp.cut
      Ebpphx.cut
      Ebraja.cut
      Ebrana.cut
      Ebrare.cut
      Ebst.cut
      Ebsu.cut
      Ebsu_h.cut
      Ecac.cut
      Ecaeel.cut
      Ecal.cut
      Ecanal.cut
      Ecanfa.cut
      Ecaucr.cut
      Eccr.cut
      Ecel.cut
      Echi.cut
      Echick.cut
      Echicken.cut
      Echisp.cut
      Echk.cut
      Echlre.cut
      Echltr.cut
      Echmp.cut
      Echnt.cut
      Echos.cut
      Echzm.cut
      Echzmrubp.cut
      Ecloab.cut
      Ecpx.cut
      Ecre.cut
      Ecrigr.cut
      Ecrisp.cut
      Ectr.cut
      Ecyapa.cut
      Edayhoff.cut
      Eddi.cut
      Eddi_h.cut
      Edicdi.cut
      Edicdi_high.cut
      Edog.cut
      Edro.cut
      Edro_h.cut
      Edrome.cut
      Edrome_high.cut
      Edrosophila.cut
      Eeca.cut
      Eeco.cut
      Eeco_h.cut
      Eecoli.cut
      Eecoli_high.cut
      Eemeni.cut
      Eemeni_high.cut
      Eemeni_mit.cut
      Eerwct.cut
      Ef1.cut
      Efish.cut
      Efmdvpolyp.cut
      Ehaein.cut
      Ehalma.cut
      Ehalsa.cut
      Eham.cut
      Ehha.cut
      Ehin.cut
      Ehma.cut
      Ehorvu.cut
      Ehum.cut
      Ehuman.cut
      Ekla.cut
      Eklepn.cut
      Eklula.cut
      Ekpn.cut
      Elacdl.cut
      Ella.cut
      Elyces.cut
      Emac.cut
      Emacfa.cut
      Emaize.cut
      Emaize_chl.cut
      Emam_h.cut
      Emammal_high.cut
      Emanse.cut
      Emarpo_chl.cut
      Emedsa.cut
      Emetth.cut
      Emixlg.cut
      Emouse.cut
      Emsa.cut
      Emse.cut
      Emta.cut
      Emtu.cut
      Emus.cut
      Emussp.cut
      Emva.cut
      Emyctu.cut
      Emze.cut
      Emzecp.cut
      Encr.cut
      Eneigo.cut
      Eneu.cut
      Eneucr.cut
      Engo.cut
      Eoncmy.cut
      Eoncsp.cut
      Eorysa.cut
      Eorysa_chl.cut
      Epae.cut
      Epea.cut
      Epet.cut
      Epethy.cut
      Epfa.cut
      Ephavu.cut
      Ephix174.cut
      Ephv.cut
      Ephy.cut
      Epig.cut
      Eplafa.cut
      Epolyomaa2.cut
      Epombe.cut
      Epombecai.cut
      Epot.cut
      Eppu.cut
      Eprovu.cut
      Epse.cut
      Epseae.cut
      Epsepu.cut
      Epsesm.cut
      Epsy.cut
      Epvu.cut
      Erab.cut
      Erabbit.cut
      Erabit.cut
      Erabsp.cut
      Erat.cut
      Eratsp.cut
      Erca.cut
      Erhile.cut
      Erhime.cut
      Erhm.cut
      Erhoca.cut
      Erhosh.cut
      Eric.cut
      Erle.cut
      Erme.cut
      Ersp.cut
      Esalsa.cut
      Esalsp.cut
      Esalty.cut
      Esau.cut
      Eschma.cut
      Eschpo.cut
      Eschpo_cai.cut
      Eschpo_high.cut
      Esco.cut
      Eserma.cut
      Esgi.cut
      Esheep.cut
      Eshp.cut
      Eshpsp.cut
      Esli.cut
      Eslm.cut
      Esma.cut
      Esmi.cut
      Esmu.cut
      Esoltu.cut
      Esoy.cut
      Esoybn.cut
      Espi.cut
      Espiol.cut
      Espn.cut
      Espo.cut
      Espo_h.cut
      Espu.cut
      Esta.cut
      Estaau.cut
      Estrco.cut
      Estrmu.cut
      Estrpn.cut
      Estrpu.cut
      Esty.cut
      Esus.cut
      Esv40.cut
      Esyhsp.cut
      Esynco.cut
      Esyncy.cut
      Esynsp.cut
      Etbr.cut
      Etcr.cut
      Eter.cut
      Etetsp.cut
      Etetth.cut
      Etheth.cut
      Etob.cut
      Etobac.cut
      Etobac_chl.cut
      Etobcp.cut
      Etom.cut
      Etrb.cut
      Etrybr.cut
      Etrycr.cut
      Evco.cut
      Evibch.cut
      Ewheat.cut
      Ewht.cut
      Exel.cut
      Exenla.cut
      Exenopus.cut
      Eyeast.cut
      Eyeast_cai.cut
      Eyeast_high.cut
      Eyeast_mit.cut
      Eyeastcai.cut
      Eyen.cut
      Eyeren.cut
      Eyerpe.cut
      Eysc.cut
      Eysc_h.cut
      Eyscmt.cut
      Eysp.cut
      Ezebrafish.cut
      Ezma.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/user/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/user/EPAM60                                            Does not exist
    File /homes/user/.embossdata/EPAM60                                Does not exist
    File /homes/user/local/share/EMBOSS/data/EPAM60                    Exists

## Command line arguments

    Find and retrieve EMBOSS data files
    Version: EMBOSS:6.5.6.0

       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)

       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 and exit. 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
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-filename] (Parameter 1) | 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 |
Additional (Optional) qualifiers
-showall | toggle | Show all potential EMBOSS data files | Toggle value Yes/No | No
-fetch | boolean | Fetch a data file | Boolean value Yes/No | No
-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). | Output file | 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. | Choose from selection list of values | 3, 5, 6
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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
--- | ---
embossupdate | Checks for more recent updates to EMBOSS
embossversion | Report the current EMBOSS version number

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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.