dbxflat

Function

Description

dbxflat indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

Usage

Command line arguments


Input file format

dbxflat reads any normal sequence USAs.

Output file format

dbxflat creates one summary file for the database and two files for each field indexed.

Data files

None.

Notes

The indexing system has been designed to allow on-the-fly updating of indexes. This feature is, however, not implemented in the current version. It will be made available in future releases.

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

DB embl [
   type: N
   dbalias: embl   (see below)
   format: embl
   method: emboss
   directory: /data/embl
   file: *.dat
   indexdirectory: /data/embl/indexes
]
The index file 'basename' given to dbxflat must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.

Fields Indexed

By default, dbxflat will index the ID name and the accession number (if present).
If they are present in your database, you may also specify that dbxflat should index the Sequence Version and GI, the words in the description, the keywords and the organism words using the '-fields' qualifier with the appropriate values.

Global Parameters

dbxflat requires that two global parameters be defined in the file emboss.defaults. These are:
SET PAGESIZE 2048
SET CACHESIZE 200
The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxflat is allowed to cache.

Resources

dbxflat will ask you for the name of a resource definition in the file emboss.defaults. This will be something like:
RES embl [
   type: Index
   idlen:  15
   acclen: 15
   svlen:  20
   keylen: 25
   deslen: 25
   orglen: 25
]
The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments