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embossdata |
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Function
Find and retrieve EMBOSS data filesDescription
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 embossdataDisplay 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/user Exists /homes/user/.embossdata Exists /homes/user/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/user/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.gff2 Efeatures.gff2protein Efeatures.gff3 Efeatures.gff3protein 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 Epkexpasy.dat Epprofile Eprior1.plib Eprior30.plib Eresidues.iub Erna.melt Esig.euk Esig.pro Etags.embl Etags.emboss Etags.gff2 Etags.gff2protein Etags.gff3 Etags.gff3protein Etags.pir Etags.protein Etags.refseqp Etags.swiss Etcode.dat Evdw.dat Ewhite-wimley.dat Matrices.nucleotide Matrices.protein Matrices.proteinstructure SSSUB edialignmat software.obo tffungi tfinsect tfother tfplant tfvertebrate tp400_dna tp400_prot tp400_trans DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_SPLICE dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_FAM dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/OBO chebi.obo eco.obo evidence_code.obo gene_ontology.1_2.obo go.obo pathway.obo ro.obo so.obo software.obo DIRECTORY: /homes/user/local/share/EMBOSS/data/REBASE embossre.enz embossre.equ embossre.ref embossre.sup DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM_HLH dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PHYLOFACTS dummyfile matrix_list.txt DIRECTORY: /homes/user/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/user/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/user/local/share/EMBOSS/data/TAXONOMY division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/AAINDEX chop780101 chop780201 chop780202 chop780203 chop780204 chop780205 chop780206 chop780207 chop780208 chop780209 chop780210 chop780211 chop780212 chop780213 chop780214 chop780215 chop780216 dummyfile kytj820101 DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_POLII dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_PBM_HOMEO dummyfile matrix_list.txt DIRECTORY: /homes/user/local/share/EMBOSS/data/JASPAR_CNE dummyfile matrix_list.txt |
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/user/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/user/EPAM60 Does not exist File /homes/user/.embossdata/EPAM60 Does not exist File /homes/user/local/share/EMBOSS/data/EPAM60 Exists |
Command line arguments
Find and retrieve EMBOSS data files
Version: EMBOSS:6.6.0.0
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
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 0Known bugs
None noted.See also
| Program name | Description |
|---|---|
| embossupdate | Check for more recent updates to EMBOSS |
| embossversion | Report the current EMBOSS version number |
Author(s)
Gary Williams formerly at:MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.