dbiflat
Function
Description
dbiflat indexes a flat file database of one or more files, and builds
EMBL CD-ROM format index files.
The resulting index-file 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.
- division.lkp is the master index file, and has a 300 byte header
containing the database name and date plus information on the record
size. This header is followed by one record for each database file,
giving the full file name for the data file, and optionally a second
sequence file.
- entryname.idx is the entry name index. It has the same 300 byte
header, mainly used to store the record size which will depend on the
size of the longest entryname in the database. Each entry is stored in
sorted alphanumeric order so that a binary search can be used to
efficiently find any record. The record also holds the file number
from division.lkp and the offsets in the data and sequence files for
that entry.
- acnum.trg holds the accession number information. The file has the
usual 300 byte header, and a sorted list of record by accession number.
Each accession number record contains the first record number in acnum.hit
and the total number of records in acnum.hit so that secondary (duplicated)
accession numbers can be searched.
- acnum.hit is a very simple file. After the usual 300 byte header,
each record simply holds the record number in entryname.idx. An
accession number search will use acnum.trg to find a start position
and number of records to read in this file, and will then simply
read the entryname.idx records for each entry in turn.
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