dbigcg
Function
Description
dbigcg indexes a GCG-format database
of one or more files, and builds EMBL CD-ROM format index files.
A GCG-format database consists of *.seq and *.ref files. The data in
the *.seq files is often compressed.
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.
Usage
Command line arguments
Input file format
dbigcg reads in a GCG-format database.
A GCG-format database consists of *.seq and *.ref files - only the *.seq
files are used. The data in these is often compressed.
Output file format
dbigcg 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 names for the reference file and 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
Having created the EMBOSS indices for this file, a database can then be
defined in the file emboss.defaults as something like:
DB embl [
type: N
format: embl
method: gcg
directory: /data/gcg/gcgembl
]
Fields Indexed
By default, dbigcg will index the ID name and the accession
number (if present).
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 errors.
Known bugs
None.
Author(s)
History
Target users
Comments