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dbifasta |
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: fasta method: emblcd directory: /data/embl/fasta ]
% dbifasta
Index a fasta database
simple : >ID
idacc : >ID ACC
gcgid : >db:ID
gcgidacc : >db:ID ACC
dbid : >db ID
ncbi : | formats
ID line format [idacc]: idacc
Database directory [.]: ../../data
Wildcard database filename [*.dat]: emrod
Database name: EMROD
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 ID line 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 | ID line format |
|
idacc | ||||||||||||
| -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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dbifasta creates four index files. All are binary but with a simple format.
| Program name | Description |
|---|---|
| dbiblast | Index a BLAST database |
| dbiflat | Index a flat file database |
| dbigcg | Index a GCG formatted database |