![]() |
dbigcg |
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.
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 ]
% dbigcg Index a GCG formatted database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GENBANK : Genbank, DDBJ PIR : NBRF Entry format [EMBL]: EMBL Database directory [.]: ../../embl Wildcard database filename [*.seq]: Database name: EMBL Release number [0.0]: Index date [00/00/00]: |
Go to the output files for this example
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 |
Mandatory qualifiers | Allowed values | Default | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
-idformat | Entry format |
|
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 | ||||||||||
-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 | Boolean value Yes/No | Yes | ||||||||||
-[no]cleanup | Clean up temporary files | Boolean value Yes/No | Yes |
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
dbigcg creates four index files. All are binary but with a simple format.
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Index a fasta database |
dbiflat | Index a flat file database |