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dbigcg
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Function
Index a GCG formatted database
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
Here is a sample session with dbigcg.
% dbigcg
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
PIR : NBRF
Entry format [EMBL]:
Database name: tembl
Database directory [.]: /nfs/disk42/pmr/emboss/test/gcgembl/
Wildcard database filename [*.seq]:
Release number [0.0]:
Index date [00/00/00]: 04/02/00
Command line arguments
Mandatory qualifiers:
-idformat menu Entry format
-directory string Database directory
-filenames string Wildcard database filename
[-dbname] string Database name
-release string Release number
-date string Index date
Optional qualifiers: (none)
Advanced qualifiers:
-fields menu Index fields
-exclude string wildcard filename(s) to exclude
-indexdirectory string Index directory
-maxindex integer Maximum index length
-sortoptions string Sort options, typically '-T .' to use
current directory for work files and '-k
1,1' to force GNU sort to use the first
field
-[no]systemsort boolean Use system sort utility
-[no]cleanup boolean Clean up temporary files
General qualifiers:
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
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Mandatory qualifiers |
Allowed values |
Default |
-idformat |
Entry format |
EMBL | (EMBL) | SWISS | (Swiss-Prot, SpTrEMBL, TrEMBLnew) | GENBANK | (Genbank, DDBJ) | PIR | (NBRF) |
|
EMBL |
-directory |
Database directory |
Any string is accepted |
. |
-filenames |
Wildcard database filename |
Any string is accepted |
*.seq |
[-dbname] (Parameter 1) |
Database name |
A string from 1 to 19 characters |
Required |
-release |
Release number |
A string up to 9 characters |
0.0 |
-date |
Index date |
Date string dd/mm/yy |
00/00/00 |
Optional qualifiers |
Allowed values |
Default |
(none) |
Advanced qualifiers |
Allowed values |
Default |
-fields |
Index fields |
acnum | (Accession number) | seqvn | (Sequence Version and GI) | des | (Description) | keyword | (Keywords) | taxon | (Taxonomy) |
|
acnum |
-exclude |
wildcard filename(s) to exclude |
Any string is accepted |
An empty string is accepted |
-indexdirectory |
Index directory |
Any string is accepted |
. |
-maxindex |
Maximum index length |
Integer 0 or more |
0 |
-sortoptions |
Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field |
Any string is accepted |
-T . -k 1,1 |
-[no]systemsort |
Use system sort utility |
Yes/No |
Yes |
-[no]cleanup |
Clean up temporary files |
Yes/No |
Yes |
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
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It exits with a status of 0 if no errors.
Known bugs
None.
Program name | Description |
dbiblast | Index a BLAST database |
dbifasta | Index a fasta database |
dbiflat | Index a flat file database |
Author(s)
This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics
Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.
History
Completed December 1999
Target users
This program is intended to be used by administrators responsible
for software and database installation and maintenance.
Comments