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dbxfasta |
Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like:
DB emrod [ type: N dbalias: emrod (see below) format: fasta method: emboss directory: /data/embl/fasta file: emrod.fasta indexdirectory: /data/embl/fasta/indexes ]The index file 'basename' given to dbxfasta must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.
% dbxfasta Database b+tree indexing for fasta file databases Basename for index files: emrod Resource name: embl 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 Release number [0.0]: Index date [00/00/00]: Processing file /ebi/services/idata/pmr/hgmp/test/data/emrod |
Go to the output files for this example
SET PAGESIZE 2048 SET CACHESIZE 200The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxfasta is allowed to cache.
RES embl [ type: Index idlen: 15 acclen: 15 svlen: 20 keylen: 25 deslen: 25 orglen: 25 ]The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set.
Standard (Mandatory) qualifiers: [-dbname] string Basename for index files [-dbresource] string Resource name -idformat menu ID line 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 -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 | |||||||||||||
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[-dbname] (Parameter 1) |
Basename for index files | A string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
[-dbresource] (Parameter 2) |
Resource name | A string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
-idformat | ID line format |
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idacc | ||||||||||||
-directory | Database directory | Directory | . | ||||||||||||
-filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||||
-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 |
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id,acc | ||||||||||||
-exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||||||||
-indexoutdir | Index directory | Output directory | . |
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Database indexing for fasta file databases |
dbiflat | Index a flat file database |
dbigcg | Index a GCG formatted database |
dbxflat | Database b+tree indexing for flat file databases |
dbxgcg | Database b+tree indexing for GCG formatted databases |