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 - only the *.seq files are used. The data in these 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.

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