| 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.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.gff
      Etags.gff3
      Etags.gff3protein
      Etags.gffprotein
      Etags.pir
      Etags.protein
      Etags.refseqp
      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

    Find and retrieve EMBOSS data files
    Version: EMBOSS:6.2.0

       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
--- | ---
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.