dbget

Function

Description

dbget retrieve database entries for a named database, data type and data identifier. A list of hyperlinks is written to the screen and to file and the data iteself is written to a specified directory. Valid database, datatypes and data identifiers are listed in the catalogue of public databases in the EMBOSS data file db.dat.

Usage

Command line arguments


Input file format

Output file format

The output file (that is written to screen) consists of a simple list of hyperlinks to the data.

The data itself (written to the specified directory) is in whatever format provided by the database, typically HTML.

Data files

The EMBOSS database information file (db.dat) must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.

Notes

The names of the queryable databases and the retrievable datatypes are listed in the catalogue of public databases in the EMBOSS data file db.dat. Data identifiers (e.g. a sequence accession number) are used to specify the data to retrieve. Datatatype names are terms from the 'data' branch of the EDAM ontology (http://edamontology.sourceforge.net/). The types of data identifier are listed under the 'Data identifier' branch of the EDAM. For example values, see the EMBOSS data file db.dat.

References

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0.

Known bugs

None.

Author(s)

This application was modified by

History

Target users

Comments