dbtell |
Please help by correcting and extending the Wiki pages.
dbtell displays on-screen information on a database with the specific ID. Optionally, the information may be written to an output file in plain text or HTML.
% dbtell tsw Display information about a public database # tsw is defined in special # access levels id: Yes query: Yes all: Yes DBNAME tsw [ format: "swiss" method: "emblcd" type: "Protein" comment: "Swissprot native format with EMBL CD-ROM index" directory: "/homes/pmr/local/share/EMBOSS/test/swiss" field: "id" field: "acc" field: "sv" field: "des" field: "org" field: "key" release: "36" edamdat: "0001230 UniProt protein sequence record" taxon: "1 all" ] |
Go to the input files for this example
Display information about a public database Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-database] string The name of the database defined locally for use by EMBOSS. (Any string) Additional (Optional) qualifiers: -full boolean [N] The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition -outfile outfile [stdout] Output file name Advanced (Unprompted) qualifiers: (none) 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 | ||||
[-database] (Parameter 1) |
string | The name of the database defined locally for use by EMBOSS. | Any string | |
Additional (Optional) qualifiers | ||||
-full | boolean | The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition | Boolean value Yes/No | No |
-outfile | outfile | Output file name | Output file | stdout |
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
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 |
The output file (plain text format) is an excerpt of and (by default) in the same format as the EMBOSS data file db.dat. The format of the file is explained in comments at the top of that file. Optionally, the data can be tabulated.
If the -html qualifier is specified, then the output will be a web page suitable for viewing in any browser.
The EMBOSS database information file (db.dat) must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.
Program name | Description |
---|---|
cachedas | Generates server cache file for DAS servers or for the DAS registry |
cachedbfetch | Generates server cache file for Dbfetch/WSDbfetch data sources |
cacheebeyesearch | Generates server cache file for EB-eye search domains |
cacheensembl | Generates server cache file for an Ensembl server |
servertell | Display information about a public server |
showdb | Displays information on configured databases |
showserver | Displays information on configured servers |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
This application was modified by
Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.