|   | dbxflat | 
| 
% dbxflat 
Index a flat file database using b+tree indices
Basename for index files: embl
Resource name: emblresource
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]: embl
Wildcard database filename [*.dat]: rod.dat
Database directory [.]: embl
        id : ID
       acc : Accession number
        sv : Sequence Version and GI
       des : Description
       key : Keywords
       org : Taxonomy
Index fields [id,acc]: 
General log output file [outfile.dbxflat]: 
 | 
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-dbname]            string     Basename for index files (Any string from 2
                                  to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     Resource name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [SWISS] Entry format (Values: EMBL (EMBL);
                                  SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); GB
                                  (Genbank, DDBJ); REFSEQ (Refseq))
   -filenames          string     [*.dat] Wildcard database filename (Any
                                  string is accepted)
   -directory          directory  [.] Database directory
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description); key (Keywords); org
                                  (Taxonomy))
   -outfile            outfile    [*.dbxflat] General log output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -indexoutdir        outdir     [.] Index file output directory
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory         string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-dbname] (Parameter 1) | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| [-dbresource] (Parameter 2) | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| -idformat | Entry format | 
 | SWISS | ||||||||||||
| -filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||||
| -directory | Database directory | Directory | . | ||||||||||||
| -fields | Index fields | 
 | id,acc | ||||||||||||
| -outfile | General log output file | Output file | <*>.dbxflat | ||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||
| (none) | |||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||
| -release | Release number | Any string up to 9 characters | 0.0 | ||||||||||||
| -date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||||||||
| Processing directory: /homes/user/test/embl/ Processing file: rod.dat entries: 6 (6) time: 0.0s (0.0s) Total time: 0.0s | 
| # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database rod.dat | 
| Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 8 Kwlimit 15 | 
| Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 5 Kwlimit 15 | 
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like:
DB embl [ type: N dbalias: embl (see below) format: embl method: emboss directory: /data/embl file: *.dat indexdirectory: /data/embl/indexes ]The index file 'basename' given to dbxflat must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.
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 dbxflat 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.
| Program name | Description | 
|---|---|
| dbiblast | Index a BLAST database | 
| dbifasta | Index a fasta file database | 
| dbiflat | Index a flat file database | 
| dbigcg | Index a GCG formatted database | 
| dbxfasta | Index a fasta file database using b+tree indices | 
| dbxgcg | Index a GCG formatted database using b+tree indices |