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 successf
ully.

   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 exis
t
File .embossdata/EPAM60                                           Does not exis
t
File /homes/pmr/EPAM60                                            Does not exis
t
File /homes/pmr/.embossdata/EPAM60                                Does not exis
t
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

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.