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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 Database name: EMBL EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GENBANK : Genbank, DDBJ PIR : NBRF Entry format [EMBL]: EMBL Database directory [.]: embl Wildcard database filename [*.seq]: Release number [0.0]: Index date [00/00/00]: |
Go to the output files for this example
Standard (Mandatory) qualifiers: [-dbname] string Database name -idformat menu Entry format -directory directory Database directory -filenames string Wildcard database filename -release string Release number -date string Index date Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -fields menu Index fields -exclude string Wildcard filename(s) to exclude -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 -indexoutdir outdir Index directory Associated qualifiers: (none) General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-dbname] (Parameter 1) |
Database name | A string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||
-idformat | Entry format |
|
EMBL | ||||||||||
-directory | Database directory | Directory | . | ||||||||||
-filenames | Wildcard database filename | Any string is accepted | *.seq | ||||||||||
-release | Release number | A string up to 9 characters | 0.0 | ||||||||||
-date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||||
(none) | |||||||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||
-fields | Index fields |
|
acnum | ||||||||||
-exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty 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 | ||||||||||
-indexoutdir | Index directory | Output directory | . |
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dbigcg creates four index files. All are binary but with a simple format.
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Database indexing for fasta file databases |
dbiflat | Index a flat file database |
dbxfasta | Database b+tree indexing for fasta file databases |
dbxflat | Database b+tree indexing for flat file databases |
dbxgcg | Database b+tree indexing for GCG formatted databases |