embossdata |
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.
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/ 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 Emolwt.dat EBLOSUMN Eangles.dat tfinsect Efeatures.gff3protein 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.gff2 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 Eresidues.iub Efeatures.protein Erna.melt Eamino.dat EBLOSUM62-12 Eantigenic.dat Efeatures.gff2protein 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/JASPAR_POLII dummyfile DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_CORE matrix_list.txt dummyfile 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 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/JASPAR_CNE 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 matrix_list.txt dummyfile 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 matrix_list.txt dummyfile DIRECTORY: /homes/pmr/local/share/EMBOSS/data/JASPAR_SPLICE dummyfile 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 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 |
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 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. 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 |
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:
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.
"'Epepcoil.dat' has been copied successfully."
Program name | Description |
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embossversion | Writes the current EMBOSS version number to a file |