
                                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 successf
ully.

   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 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 (* 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.
