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dbiflat |
A flat file database is a database in one of the native formats: EMBL, Swiss-Prot or GenBank, as distributed by the EBI, NCBI, or DDBJ. (It is called a 'flat' file to distinguish it from the complex relational database formats that this data is held in before being written to files and distributed.)
Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like:
DB emrod [ type: N format: embl method: emblcd directory: /data/embl ]
% dbiflat
Index a flat file database
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
REFSEQ : Refseq
Entry format [SWISS]: EMBL
Database directory [.]: ../../embl
Wildcard database filename [*.dat]: rod.dat
Database name: EMBL
Release number [0.0]:
Index date [00/00/00]:
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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
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 required and optional values
-debug boolean Write debug output to program.dbg
-acdlog boolean Write ACD processing log to program.acdlog
-acdpretty boolean Rewrite ACD file as program.acdpretty
-acdtable boolean Write HTML table of options
-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
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| Mandatory qualifiers | Allowed values | Default | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -idformat | Entry format |
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SWISS | ||||||||||
| -directory | Database directory | Any string is accepted | . | ||||||||||
| -filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||
| [-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 | ||||||||||
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dbiflat 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 |
| dbigcg | Index a GCG formatted database |