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dbifasta |
% dbifasta Index a fasta database simple : >ID idacc : >ID ACC gcgid : >db:ID gcgidacc : >db:ID ACC ncbi : >blah|...[|ACC]|ID ID line format [idacc]: idacc Database name: wormpep Database directory [.]: /data/worm/ Wildcard database filename [*.dat]: wormpep Release number [0.0]: 1.0 Index date [00/00/00]: 04/02/00
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 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 | ID line format |
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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 | Yes/No | Yes | ||||||||||||
-[no]cleanup | Clean up temporary files | Yes/No | Yes |
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbiflat | Index a flat file database |
dbigcg | Index a GCG formatted database |