dbiflat

Function

Description

dbiflat indexes a flat file database of one or more files, and builds EMBL CD-ROM format index files. This format is used by the software on the EMBL database CD-ROM distribution and by the Staden package in addition to EMBOSS, and appears to be the most generally used and publicly available index file format for these databases.

A flat file database is a database in one of the native formats: EMBL, Swiss-Prot or GenBank, as distributed by the EBI, NCBI, or DDBJ. (It is called a 'flat' file to distinguish it from the complex relational database formats that this data is held in before being written to files and distributed.)

Usage

Command line arguments


Input file format

'flat' files (native distribution format) of a protein or nucleic sequence database.

Output file format

dbiflat creates four index files. All are binary but with a simple format.

Data files

None.

Notes

The indexing method depends on each entry having a unique entry name. No allowance is made for two entries with the same name so it is not possible to index EMBL and EMBLNEW together.

Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like:

DB emrod [
   type: N
   format: embl
   method: emblcd
   directory: /data/embl
]  

Fields Indexed

By default, dbiflat will index the ID name and the accession number.
If they are present in your database, you may also specify that dbiflat should index the Sequence Version and GI number, the Keywords and Taxonomy names and the words in the description by using the '-fields' qualifier with the appropriate values.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0 if no problems.

Known bugs

None.

Author(s)

History

Target users

Comments