|   | 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
Database name: EMBL
      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
Release number [0.0]: 
Index date [00/00/00]: 
General log output file [outfile.dbiflat]: 
 | 
Go to the output files for this example
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   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database 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))
   -directory          directory  [.] Database directory
   -filenames          string     [*.dat] Wildcard database filename (Any
                                  string is accepted)
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -outfile            outfile    [*.dbiflat] General log output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       [acc] Index fields (Values: acc (acnum
                                  accession number index); sv (seqvn sequence
                                  version and gi number index); des (des
                                  description index); key (keyword keywords
                                  index); org (taxon taxonomy and organism
                                  index))
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -maxindex           integer    [0] Maximum index length (Integer 0 or more)
   -sortoptions        string     [-T . -k 1,1] 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)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -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 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 dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-dbname] (Parameter 1) | Database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||
| -idformat | Entry format | 
 | SWISS | ||||||||||
| -directory | Database directory | Directory | . | ||||||||||
| -filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||
| -release | Release number | Any string up to 9 characters | 0.0 | ||||||||||
| -date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||
| -outfile | General log output file | Output file | <*>.dbiflat | ||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||
| (none) | |||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||
| -fields | Index fields | 
 | acc | ||||||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty 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 | ||||||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||||||
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########################################
# Program: dbiflat
# Rundate: Sun 15 Jul 2007 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/07
# CurrentDirectory: /homes/user/test/qa/dbiflat-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiflat-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/embl/
# DirectoryPath: /homes/user/test/embl/
# Filenames: rod.dat
# Exclude: 
# Files: 1
#   File 1: /homes/user/test/embl/rod.dat
########################################
# Commandline: dbiflat
#    -dbname EMBL
#    -idformat EMBL
#    -directory ../../embl
#    -filenames rod.dat
########################################
filename: 'rod.dat'
    id: 6
   acc: 9
Index acc: maxlen 6 items 7
Total 1 files 6 entries (0 duplicates)
 | 
dbiflat creates four index files. All are binary but with a simple format.
| Program name | Description | 
|---|---|
| dbiblast | Index a BLAST database | 
| dbifasta | Database indexing for fasta file databases | 
| dbigcg | Index a GCG formatted database | 
| dbxfasta | Database b+tree indexing for fasta file databases | 
| dbxflat | Database b+tree indexing for flat file databases | 
| dbxgcg | Database b+tree indexing for GCG formatted databases |