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/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/

  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
  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.gff
  Efeatures.gff2
  Efeatures.gff2protein
  Efeatures.gff3
  Efeatures.gff3protein
  Efeatures.gffprotein
  Efeatures.pir
  Efeatures.protein
  Efeatures.swiss
  Efreqs.dat
  Ehet.dat
  Ehth.dat
  Ehth87.dat
  Emass.dat
  Emassmod.dat
  Ememe.dat
  Emethylsites.dat
  Emolwt.dat
  Emwfilter.dat
  Enakai.dat
  Epepcoil.dat
  Epk.dat
  Epprofile
  Eprior1.plib
  Eprior30.plib
  Eresidues.iub
  Erna.melt
  Esig.euk
  Esig.pro
  Etags.embl
  Etags.emboss
  Etags.gff
  Etags.gff3
  Etags.gff3protein
  Etags.gffprotein
  Etags.pir
  Etags.protein
  Etags.swiss
  Etcode.dat
  Evdw.dat
  Ewhite-wimley.dat
  Matrices.nucleotide
  Matrices.protein
  Matrices.proteinstructure
  SSSUB
  edialignmat
  embossre.equ
  tffungi
  tfinsect
  tfother
  tfplant
  tfvertebrate
  tp400_dna
  tp400_prot
  tp400_trans


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
  dummyfile
  matrix_list.txt


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

  dummyfile


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

  alts910101
  andn920101
  argp820101
  argp820102
  argp820103
  aurr980101
  aurr980102
  aurr980103
  aurr980104
  aurr980105
  aurr980106
  aurr980107
  aurr980108
  aurr980109
  aurr980110
  aurr980111
  aurr980112
  aurr980113
  aurr980114
  aurr980115
  aurr980116
  aurr980117
  aurr980118
  aurr980119
  aurr980120
  avbf000101
  avbf000102
  avbf000103
  avbf000104
  avbf000105
  avbf000106
  avbf000107
  avbf000108
  avbf000109
  azae970101
  azae970102
  baek050101
  basu010101
  basu050101
  basu050102
  basu050103
  begf750101
  begf750102
  begf750103
  bens940101
  bens940102
  bens940103
  bens940104
  betm990101
  bhar880101
  bigc670101
  biov880101
  biov880102
  blaj010101
  blam930101
  blas910101
  bonm030101
  bonm030102
  bonm030103
  bonm030104
  bonm030105
  bonm030106
  broc820101
  broc820102
  brys930101
  bulh740101
  bulh740102
  buna790101
  buna790102
  buna790103
  bura740101
  bura740102
  casg920101
  cedj970101
  cedj970102
  cedj970103
  cedj970104
  cedj970105
  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
  corj870101
  corj870102
  corj870103
  corj870104
  corj870105
  corj870106
  corj870107
  corj870108
  cosi940101
  cowr900101
  craj730101
  craj730102
  craj730103
  crog050101
  csem940101
  dawd720101
  daym780101
  daym780201
  daym780301
  daym780302
  desm900101
  desm900102
  digm050101
  dosz010101
  dosz010102
  dosz010103
  dosz010104
  dummyfile
  eisd840101
  eisd860101
  eisd860102
  eisd860103
  engd860101
  fasg760101
  fasg760102
  fasg760103
  fasg760104
  fasg760105
  fasg890101
  fauj830101
  fauj880101
  fauj880102
  fauj880103
  fauj880104
  fauj880105
  fauj880106
  fauj880107
  fauj880108
  fauj880109
  fauj880110
  fauj880111
  fauj880112
  fauj880113
  fend850101
  fina770101
  fina910101
  fina910102
  fina910103
  fina910104
  fitw660101
  fodm020101
  fuks010101
  fuks010102
  fuks010103
  fuks010104
  fuks010105
  fuks010106
  fuks010107
  fuks010108
  fuks010109
  fuks010110
  fuks010111
  fuks010112
  garj730101
  geim800101
  geim800102
  geim800103
  geim800104
  geim800105
  geim800106
  geim800107
  geim800108
  geim800109
  geim800110
  geim800111
  geod900101
  geor030101
  geor030102
  geor030103
  geor030104
  geor030105
  geor030106
  geor030107
  geor030108
  geor030109
  giag010101
  goda950101
  gold730101
  gold730102
  gong920101
  grar740101
  grar740102
  grar740103
  grar740104
  guod860101
  guyh850101
  guyh850102
  guyh850103
  guyh850104
  guyh850105
  hary940101
  hens920101
  hens920102
  hens920103
  hens920104
  hopa770101
  hopt810101
  hutj700101
  hutj700102
  hutj700103
  isoy800101
  isoy800102
  isoy800103
  isoy800104
  isoy800105
  isoy800106
  isoy800107
  isoy800108
  jacr890101
  janj780101
  janj780102
  janj780103
  janj790101
  janj790102
  johm930101
  jond750101
  jond750102
  jond920101
  jond920102
  jond920103
  jond940101
  jukt750101
  junj780101
  jurd980101
  kanm000101
  kanm800101
  kanm800102
  kanm800103
  kanm800104
  kapo950101
  karp850101
  karp850102
  karp850103
  keso980101
  keso980102
  khag800101
  kida850101
  kimc930101
  klep840101
  koep990101
  koep990102
  kola920101
  kola930101
  kosj950101
  kosj950102
  kosj950103
  kosj950104
  kosj950105
  kosj950106
  kosj950107
  kosj950108
  kosj950109
  kosj950110
  kosj950111
  kosj950112
  kosj950113
  kosj950114
  kosj950115
  kriw710101
  kriw790101
  kriw790102
  kriw790103
  kuhl950101
  kums000101
  kums000102
  kums000103
  kums000104
  kytj820101
  lawe840101
  levj860101
  levm760101
  levm760102
  levm760103
  levm760104
  levm760105
  levm760106
  levm760107
  levm780101
  levm780102
  levm780103
  levm780104
  levm780105
  levm780106
  lewp710101
  lifs790101
  lifs790102
  lifs790103
  link010101
  liwa970101
  lutr910101
  lutr910102
  lutr910103
  lutr910104
  lutr910105
  lutr910106
  lutr910107
  lutr910108
  lutr910109
  manp780101
  maxf760101
  maxf760102
  maxf760103
  maxf760104
  maxf760105
  maxf760106
  mcla710101
  mcla720101
  mcmt640101
  meej800101
  meej800102
  meej810101
  meej810102
  mehp950101
  mehp950102
  mehp950103
  meih800101
  meih800102
  meih800103
  micc010101
  mirl960101
  mits020101
  miys850101
  miys850102
  miys850103
  miys930101
  miys960101
  miys960102
  miys960103
  miys990101
  miys990102
  miys990103
  miys990104
  miys990105
  miys990106
  miys990107
  miyt790101
  mohr870101
  monm990101
  monm990201
  moog990101
  muet010101
  muet020101
  muet020102
  munv940101
  munv940102
  munv940103
  munv940104
  munv940105
  nadh010101
  nadh010102
  nadh010103
  nadh010104
  nadh010105
  nadh010106
  nadh010107
  nagk730101
  nagk730102
  nagk730103
  nakh900101
  nakh900102
  nakh900103
  nakh900104
  nakh900105
  nakh900106
  nakh900107
  nakh900108
  nakh900109
  nakh900110
  nakh900111
  nakh900112
  nakh900113
  nakh920101
  nakh920102
  nakh920103
  nakh920104
  nakh920105
  nakh920106
  nakh920107
  nakh920108
  naod960101
  ngpc000101
  niek910101
  niek910102
  nisk800101
  nisk860101
  nozy710101
  ogak980101
  olsk800101
  onek900101
  onek900102
  oobm770101
  oobm770102
  oobm770103
  oobm770104
  oobm770105
  oobm850101
  oobm850102
  oobm850103
  oobm850104
  oobm850105
  ovej920101
  ovej920102
  ovej920103
  ovej920104
  ovej920105
  palj810101
  palj810102
  palj810103
  palj810104
  palj810105
  palj810106
  palj810107
  palj810108
  palj810109
  palj810110
  palj810111
  palj810112
  palj810113
  palj810114
  palj810115
  palj810116
  parb960101
  parb960102
  parj860101
  pars000101
  pars000102
  pliv810101
  ponj960101
  ponp800101
  ponp800102
  ponp800103
  ponp800104
  ponp800105
  ponp800106
  ponp800107
  ponp800108
  ponp930101
  pram820101
  pram820102
  pram820103
  pram900101
  pram900102
  pram900103
  pram900104
  prla000101
  prla000102
  ptio830101
  ptio830102
  punt030101
  punt030102
  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
  qu_c930101
  qu_c930102
  qu_c930103
  quib020101
  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
  rier950101
  risj880101
  robb760101
  robb760102
  robb760103
  robb760104
  robb760105
  robb760106
  robb760107
  robb760108
  robb760109
  robb760110
  robb760111
  robb760112
  robb760113
  robb790101
  robb790102
  rosg850101
  rosg850102
  rosm880101
  rosm880102
  rosm880103
  rosm880104
  rosm880105
  rusr970101
  rusr970102
  rusr970103
  simk990101
  simk990102
  simk990103
  simk990104
  simk990105
  simz760101
  skoj000101
  skoj000102
  skoj970101
  snep660101
  snep660102
  snep660103
  snep660104
  suem840101
  suem840102
  suym030101
  swer830101
  takk010101
  tans760101
  tans760102
  tans770101
  tans770102
  tans770103
  tans770104
  tans770105
  tans770106
  tans770107
  tans770108
  tans770109
  tans770110
  thop960101
  tobd000101
  tobd000102
  tsaj990101
  tsaj990102
  tude900101
  vasm830101
  vasm830102
  vasm830103
  velv850101
  venm980101
  vent840101
  vheg790101
  vinm940101
  vinm940102
  vinm940103
  vinm940104
  vogg950101
  warp780101
  weba780101
  weil970101
  weil970102
  werd780101
  werd780102
  werd780103
  werd780104
  wilm950101
  wilm950102
  wilm950103
  wilm950104
  wimw960101
  woec730101
  wolr790101
  wolr810101
  wols870101
  wols870102
  wols870103
  yanj020101
  yutk870101
  yutk870102
  yutk870103
  yutk870104
  zasb820101
  zhac000101
  zhac000102
  zhac000103
  zhac000104
  zhac000105
  zhac000106
  zhoh040101
  zhoh040102
  zhoh040103
  zimj680101
  zimj680102
  zimj680103
  zimj680104
  zimj680105


DIRECTORY: /homes/pmr/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


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

  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
  dummyfile
  matrix_list.txt


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

  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
  dummyfile
  matrix_list.txt


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

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


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

  dummyfile

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:

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 Reports 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.