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embossdata |
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:
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.
Display 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/ EGC.10 EGC.11 EGC.12 EGC.13 EGC.14 EGC.15 EGC.16 EGC.21 EGC.22 EGC.23 EPAM10 EPAM20 EPAM30 EPAM40 EPAM50 EPAM60 EPAM70 EPAM80 EPAM90 edialignmat Eenergy.dat EDNAMAT Etags.swiss Matrices.proteinstructure Emass.dat Etags.gffprotein EGC.txt Ehth87.dat Eaa_hydropathy.dat Enakai.dat EGC.0 EGC.1 EGC.2 EGC.3 EGC.4 EGC.5 EGC.6 EGC.9 Eangles_tri.dat Epprofile Efreqs.dat Emwfilter.dat ENUC.4.2 ENUC.4.4 Etags.embl Etags.gff3 tp400_trans Etags.gff Etags.pir EPAM100 EPAM110 EPAM120 EPAM130 EPAM140 EPAM150 EPAM160 EPAM170 EPAM180 EPAM190 EPAM200 EPAM210 EPAM220 EPAM230 EPAM240 EPAM250 EPAM260 EPAM270 EPAM280 EPAM290 EPAM300 EPAM310 EPAM320 EPAM330 EPAM340 EPAM350 EPAM360 EPAM370 EPAM380 EPAM390 EPAM400 EPAM410 EPAM420 EPAM430 EPAM440 EPAM450 EPAM460 EPAM470 EPAM480 EPAM490 EPAM500 Ehet.dat Evdw.dat Edna.melt Eaa_properties.dat Eamino.dat~ EBLOSUMN Eangles.dat tfinsect tffungi Etcode.dat tfother tfplant Ehth.dat Etags.emboss tp400_dna Ebases.iub Efeatures.gff Efeatures.pir Etags.protein Eaa_acc_surface.dat Epepcoil.dat Ememe.dat Efeatures.gffprotein Eprior1.plib Efeatures.embl Efeatures.gff3 EBLOSUM30 EBLOSUM35 EBLOSUM40 EBLOSUM45 EBLOSUM50 EBLOSUM55 EBLOSUM60 EBLOSUM62 EBLOSUM65 EBLOSUM70 EBLOSUM75 EBLOSUM80 EBLOSUM85 EBLOSUM90 EDNAFULL Emassmod.dat Efeatures.emboss Matrices.nucleotide Epk.dat tfvertebrate Efeatures.protein Erna.melt Eamino.dat EBLOSUM62-12 Eantigenic.dat Efeatures.swiss Eembl.ior tp400_prot Eprior30.plib Esig.euk Esig.pro EGC.index Ewhite-wimley.dat Matrices.protein embossre.equ Edayhoff.freq DIRECTORY: /homes/pmr/local/share/EMBOSS/data/REBASE dummyfile embossre.enz embossre.equ embossre.ref embossre.sup DIRECTORY: /homes/pmr/local/share/EMBOSS/data/AAINDEX dummyfile kytj820101 chop780101 chop780201 chop780202 chop780203 chop780204 chop780205 chop780206 chop780207 chop780208 chop780209 chop780210 chop780211 chop780212 chop780213 chop780214 chop780215 chop780216 DIRECTORY: /homes/pmr/local/share/EMBOSS/data/CODONS EAedes_aegypti.cut Ecyapa.cut Eerwct.cut Ehuman.cut Eratsp.cut Esta.cut Ecaeel.cut EAedes_atropalpus.cut Estaau.cut Edrome_high.cut Echmp.cut Eyerpe.cut Ecrisp.cut Efish.cut Esty.cut Ehalsa.cut Emyctu.cut Esus.cut Echnt.cut Edicdi.cut Echos.cut EAmblyomma_americanum.cut Encr.cut Epolyomaa2.cut EAphrodite_aculeata.cut Ebommo.cut Eysc_h.cut Eschpo_high.cut Etob.cut Eneu.cut Etom.cut Ephix174.cut Emedsa.cut Eanidmit.cut Emsa.cut Engo.cut Emse.cut Epethy.cut Esynsp.cut Emta.cut Etrb.cut Eani_h.cut Etheth.cut Echicken.cut Emtu.cut Emva.cut Ebpphx.cut Eschpo_cai.cut Emus.cut Eacc.cut Eorysa.cut Eham.cut Ebraja.cut Eshpsp.cut Emanse.cut Emaize_chl.cut Edro_h.cut Echzm.cut Echzmrubp.cut Emze.cut Evibch.cut Epombecai.cut EAstacus_astacus.cut Ebrana.cut Erhoca.cut Eemeni_high.cut Evco.cut Ehha.cut Eanasp.cut Ebacme.cut Esyhsp.cut Erabit.cut Eneigo.cut Ecanal.cut Ehin.cut Elyces.cut Eklepn.cut Ebrare.cut Eyscmt.cut Epseae.cut Eemeni_mit.cut Ehma.cut Eani.cut Ecanfa.cut Emixlg.cut Ecaucr.cut Epae.cut Ephavu.cut Ebovin.cut Ehorvu.cut Ebacst.cut Ebacsu.cut Echlre.cut Epea.cut Edrome.cut Esheep.cut Erabsp.cut Epfa.cut Esalsa.cut Easn.cut Ebacsu_high.cut Eecoli_high.cut Eath.cut Epet.cut Ebja.cut Emacfa.cut EAcanthocheilonema_viteae.cut Esalsp.cut Eyeast_cai.cut Eatu.cut Echltr.cut Eoncmy.cut Eavi.cut Ecac.cut Eemeni.cut Esalty.cut Ehum.cut Eprovu.cut Epig.cut Esoybn.cut Ecal.cut Ephv.cut Ephy.cut Ebme.cut Erhosh.cut Ebna.cut Ewht.cut Ebly.cut Ebmo.cut Ef1.cut Emetth.cut EAnadara_trapezia.cut Ebovsp.cut Eccr.cut Erhile.cut Eplafa.cut Erhime.cut Ebov.cut Ecel.cut Eoncsp.cut Epsepu.cut Estrco.cut Echi.cut Epot.cut Echk.cut Epsesm.cut Etetsp.cut Eklula.cut Etetth.cut Ebsu_h.cut Ebst.cut Ebsu.cut Emaize.cut Eppu.cut Exel.cut Emouse.cut Eagrtu.cut Epse.cut Eserma.cut Eazovi.cut Epsy.cut Ewheat.cut Eyeast.cut Eacica.cut Erab.cut Eddi.cut EAedes_albopictus.cut Espo_h.cut Epvu.cut Etobac.cut Erat.cut Erca.cut Eaidlav.cut Ezebrafish.cut Ecpx.cut Ecre.cut Cut.index Estrmu.cut Efmdvpolyp.cut Etobcp.cut Eyeastcai.cut Estrpn.cut Eyen.cut Ectr.cut Estrpu.cut Emzecp.cut Exenopus.cut Edrosophila.cut Eeco_h.cut Eorysa_chl.cut Erhm.cut Eric.cut Ekla.cut Earath.cut Eeca.cut Echick.cut EAedes.cut Eeco.cut Erle.cut Edog.cut Emam_h.cut Eyeast_high.cut Erme.cut Esau.cut Esoltu.cut Emammal_high.cut Esco.cut Ekpn.cut Edro.cut Eadenovirus5.cut Exenla.cut Eadenovirus7.cut Etobac_chl.cut Elacdl.cut Esgi.cut EDictyostelium_discoideum.cut Erabbit.cut Eddi_h.cut Eshp.cut Ersp.cut Eysc.cut Ella.cut Ecrigr.cut Emac.cut Emarpo_chl.cut Eecoli.cut Edicdi_high.cut Eysp.cut Esv40.cut Eyeren.cut Edayhoff.cut Etrybr.cut Ehaein.cut Etrycr.cut Esli.cut Esynco.cut Esma.cut Eslm.cut Eschma.cut Esmi.cut Esyncy.cut Ezma.cut Etbr.cut Esmu.cut Etcr.cut Ehalma.cut Eneucr.cut Echisp.cut Espi.cut Emussp.cut Ecloab.cut Epombe.cut Espiol.cut Esoy.cut Espn.cut Espo.cut Eter.cut Eyeast_mit.cut Eschpo.cut Espu.cut |
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 |
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 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 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 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 |
"'Epepcoil.dat' has been copied successfully."
| Program name | Description |
|---|---|
| embossversion | Writes the current EMBOSS version number |