embossdata

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Function

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

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 Exists /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/ DRCAT.dat EBLOSUM30 EBLOSUM35 EBLOSUM40 EBLOSUM45 EBLOSUM50 EBLOSUM55 EBLOSUM60 EBLOSUM62 EBLOSUM62-12 EBLOSUM65 EBLOSUM70 EBLOSUM75 EBLOSUM80 EBLOSUM85 EBLOSUM90 EBLOSUMN EDAM.obo EDNAFULL EDNAMAT EDNASIMPLE EGC.0 EGC.1 EGC.10 EGC.11 EGC.12 EGC.13 EGC.14 EGC.15 EGC.16 EGC.2 EGC.21 EGC.22 EGC.23 EGC.3 EGC.4 EGC.5 EGC.6 EGC.9 EGC.index EGC.txt ENUC.4.2 ENUC.4.4 EPAM10 EPAM100 EPAM110 EPAM120 EPAM130 EPAM140 EPAM150 EPAM160 EPAM170 EPAM180 EPAM190 EPAM20 EPAM200 EPAM210 EPAM220 EPAM230 EPAM240 EPAM250 EPAM260 EPAM270 EPAM280 EPAM290 EPAM30 EPAM300 EPAM310 EPAM320 EPAM330 EPAM340 EPAM350 EPAM360 EPAM370 EPAM380 EPAM390 EPAM40 EPAM400 EPAM410 EPAM420 EPAM430 EPAM440 EPAM450 EPAM460 EPAM470 EPAM480 EPAM490 EPAM50 EPAM500 EPAM60 EPAM70 EPAM80 EPAM90 Eaa_acc_surface.dat Eaa_hydropathy.dat Eaa_properties.dat Eamino.dat Eangles.dat Eangles_tri.dat Eantigenic.dat Ebases.iub Edayhoff.freq Edna.melt Eembl.ior Eenergy.dat Efeatures.embl Efeatures.emboss Efeatures.gff Efeatures.gff2 Efeatures.gff2protein Efeatures.gff3 Efeatures.gff3protein Efeatures.gff3~ 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.gff2 Etags.gff2protein 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 dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_POLII dummyfile matrix_list.txt 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/JASPAR_PBM_HLH dummyfile matrix_list.txt 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 matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_FAM dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_CORE MA0070.1.pfm MA0071.1.pfm MA0072.1.pfm MA0073.1.pfm MA0074.1.pfm MA0075.1.pfm MA0076.1.pfm MA0077.1.pfm MA0078.1.pfm MA0079.1.pfm MA0079.2.pfm dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/REBASE dummyfile embossre.enz embossre.equ embossre.ref embossre.sup DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_PBM dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_PBM_HOMEO dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_CNE dummyfile matrix_list.txt DIRECTORY: /homes/pmr/local/share/EMBOSS/data/OBO evidence_code.obo gene_ontology.1_2.obo pathway.obo ro.obo so.obo DIRECTORY: /homes/pmr/local/share/EMBOSS/data/TAXONOMY division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp

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:6.4.0.0

   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

Output file format

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

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

-outfile option

-reject option

References

Warnings

Diagnostic Error Messages

"'Epepcoil.dat' has been copied successfully."

Exit status

Known bugs

See also

Author(s)

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

History

Target users

Comments