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embossdata |
Function
Finds or fetches data files read by EMBOSS programsDescription
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 embossdataDisplay the directories searched for EMBOSS data files:
% embossdata Finds or fetches data files read by EMBOSS programs Data file name: # The following directories can contain EMBOSS data files. # They are searched in the following order until the file is found. # If the directory does not exist, then this is noted below. # '.' is the UNIX name for your current working directory. . Exists .embossdata Does not exist /homes/pmr Exists /homes/pmr/.embossdata Does not exist /homes/pmr/local/share/EMBOSS/data/ Exists |
Example 2
Display the names of data files in all of the possible data directories: This is run on a small test system and so the results will probably be different when you run this.
% embossdata -showall Finds or fetches data files read by EMBOSS programs Data file name: DIRECTORY: /homes/pmr/local/share/EMBOSS/data/ 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 EGC.index EGC.txt Matrices.nucleotide Matrices.protein Matrices.proteinstructure 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 Cut.index 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 Eacica.cut Ef1.cut Efish.cut Efmdvpolyp.cut Eham.cut Ehha.cut Ehin.cut Ehma.cut Ehum.cut Eagrtu.cut Ekla.cut Ekpn.cut Ella.cut Emac.cut Eanasp.cut Emam_h.cut Emixlg.cut Earath.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 Eazovi.cut Epae.cut Ebacme.cut Epet.cut Epfa.cut Ephix174.cut Ephv.cut Ephy.cut Ebacst.cut Epolyomaa2.cut Epombe.cut Epombecai.cut Epot.cut Eppu.cut Epse.cut Epsy.cut Epvu.cut Erab.cut Erabbit.cut Erabsp.cut Ebacsu.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 Ebommo.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 Ebovin.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 Ebacsu_high.cut Ebpphx.cut Ebraja.cut Ebrana.cut Ebrare.cut Ecaeel.cut Ecanal.cut Ecanfa.cut Ecaucr.cut Echick.cut Echlre.cut Echltr.cut Ecloab.cut Ecrigr.cut Ecyapa.cut Edicdi.cut Edicdi_high.cut Edrome.cut Edrome_high.cut Eecoli.cut Eecoli_high.cut Eemeni.cut Eemeni_mit.cut Eemeni_high.cut Eerwct.cut Ehaein.cut Ehalma.cut Ehalsa.cut Ehorvu.cut Ehuman.cut Eklepn.cut Eklula.cut Elacdl.cut Elyces.cut Emacfa.cut Emaize.cut Emaize_chl.cut Emammal_high.cut Emanse.cut Emarpo_chl.cut Emedsa.cut Emetth.cut Emouse.cut Emyctu.cut Eneigo.cut Eneucr.cut Eoncmy.cut Eorysa.cut Eorysa_chl.cut Epea.cut Epethy.cut Ephavu.cut Epig.cut Eplafa.cut Eprovu.cut Epseae.cut Epsepu.cut Epsesm.cut Erabit.cut Erat.cut Erhile.cut Erhime.cut Erhoca.cut Erhosh.cut Esalsa.cut Esalty.cut Eschma.cut Eschpo.cut Eschpo_cai.cut Eschpo_high.cut Eserma.cut Esheep.cut Esoltu.cut Esoybn.cut Espiol.cut Estaau.cut Estrco.cut Estrmu.cut Estrpn.cut Estrpu.cut Esyncy.cut Esynco.cut Etetth.cut Etheth.cut Etobac.cut Etobac_chl.cut Etrybr.cut Etrycr.cut Evibch.cut Ewheat.cut Exenla.cut Eyeast.cut Eyeast_cai.cut Eyeast_high.cut Eyeast_mit.cut Eyeren.cut Eyerpe.cut Eoncsp.cut Esv40.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 Epepcoil.dat Finds or fetches data files read by EMBOSS programs 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 Finds or fetches data files read by EMBOSS programs # The following directories can contain EMBOSS data files. # They are searched in the following order until the file is found. # If the directory does not exist, then this is noted below. # '.' is the UNIX name for your current working directory. File ./EPAM60 Does not 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.
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] (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
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 0Known 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