|   | dbiflat | 
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The resulting index-file format is used by the software on the EMBL database CD-ROM distribution and by the Staden package in addition to EMBOSS, and appears to be the most generally used and publicly available index file format for these databases.
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.)
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% 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
| 
Index a flat file database
Version: EMBOSS:6.6.0.0
   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)
   -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)
   -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)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory
   Associated qualifiers:
   "-directory" associated qualifiers
   -extension          string     Default file extension
   "-outfile" associated qualifiers
   -odirectory         string     Output directory
   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension
   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 and exit. 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
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||
| [-dbname] (Parameter 1) | string | Database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||
| -idformat | list | Entry format | 
 | SWISS | ||||||||||
| -directory | directory | Database directory | Directory | . | ||||||||||
| -filenames | string | Wildcard database filename | Any string | *.dat | ||||||||||
| -release | string | Release number | Any string up to 9 characters | 0.0 | ||||||||||
| -date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||
| -outfile | outfile | General log output file | Output file | <*>.dbiflat | ||||||||||
| Additional (Optional) qualifiers | ||||||||||||||
| (none) | ||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||
| -fields | list | Index fields | 
 | acc | ||||||||||
| -exclude | string | Wildcard filename(s) to exclude | Any string | |||||||||||
| -maxindex | integer | Maximum index length | Integer 0 or more | 0 | ||||||||||
| -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 | Any string | -T . -k 1,1 | ||||||||||
| -[no]systemsort | boolean | Use system sort utility | Boolean value Yes/No | Yes | ||||||||||
| -[no]cleanup | boolean | Clean up temporary files | Boolean value Yes/No | Yes | ||||||||||
| -indexoutdir | outdir | Index file output directory | Output directory | . | ||||||||||
| Associated qualifiers | ||||||||||||||
| "-directory" associated directory qualifiers | ||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||
| "-outfile" associated outfile qualifiers | ||||||||||||||
| -odirectory | string | Output directory | Any string | |||||||||||
| "-indexoutdir" associated outdir qualifiers | ||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||
| General qualifiers | ||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||
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########################################
# Program: dbiflat
# Rundate: Mon 15 Jul 2013 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/13
# 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.
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 ]
| Program name | Description | 
|---|---|
| dbiblast | Index a BLAST database | 
| dbifasta | Index a fasta file database | 
| dbigcg | Index a GCG formatted database | 
| dbxcompress | Compress an uncompressed dbx index | 
| dbxedam | Index the EDAM ontology using b+tree indices | 
| dbxfasta | Index a fasta file database using b+tree indices | 
| dbxflat | Index a flat file database using b+tree indices | 
| dbxgcg | Index a GCG formatted database using b+tree indices | 
| dbxobo | Index an obo ontology using b+tree indices | 
| dbxreport | Validate index and report internals for dbx databases | 
| dbxresource | Index a data resource catalogue using b+tree indices | 
| dbxstat | Dump statistics for dbx databases | 
| dbxtax | Index NCBI taxonomy using b+tree indices | 
| dbxuncompress | Uncompress a compressed dbx index | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.