EMBOSS: dbxflat

| dbxflat

## Function

Index a flat file database using b+tree indices

## Description

dbxflat indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

## Usage

Here is a sample session with 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

## Command line arguments

       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 |
EMBL | (EMBL)
SWISS | (Swiss-Prot, SpTrEMBL, TrEMBLnew)
GB | (Genbank, DDBJ)
REFSEQ | (Refseq)
| SWISS
-filenames | Wildcard database filename | Any string is accepted | *.dat
-directory | Database directory | Directory | .
-fields | Index fields |
id | (ID)
acc | (Accession number)
sv | (Sequence Version and GI)
des | (Description)
key | (Keywords)
org | (Taxonomy)
| 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 | .

## Input file format

dbxflat reads any normal sequence USAs.

## Output file format

dbxflat creates one summary file for the database and two files for each field indexed.

- dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
- dbalias.xid is the B+tree index file for the ID names. It is a binary file.
- dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

### Output files for usage example

### File: outfile.dbxflat

    Processing directory: /homes/user/test/embl/
    Processing file: rod.dat entries: 6 (6) time: 0.0s (0.0s)
    Total time: 0.0s

### File: embl.ent

    # Number of files: 1
    # Release: 0.0
    # Date:    00/00/00
    Single filename database
    rod.dat

### File: embl.pxac

    Order     71
    Fill      46
    Pagesize  2048
    Level     0
    Cachesize 100
    Order2    99
    Fill2     101
    Count     8
    Kwlimit   15

### File: embl.pxid

    Order     71
    Fill      46
    Pagesize  2048
    Level     0
    Cachesize 100
    Order2    99
    Fill2     101
    Count     5
    Kwlimit   15

### File: embl.xac

This file contains non-printing characters and so cannot be displayed here.

### File: embl.xid

This file contains non-printing characters and so cannot be displayed here.

## Data files

None.

## Notes

The indexing system has been designed to allow on-the-fly updating of indexes. This feature is, however, not implemented in the current version. It will be made available in future releases.

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.

### Fields Indexed

By default, dbxflat will index the ID name and the accession number (if present).
If they are present in your database, you may also specify that dbxflat should index the Sequence Version and GI, the words in the description, the keywords and the organism words using the '-fields' qualifier with the appropriate values.

## Global Parameters

dbxflat requires that two global parameters be defined in the file emboss.defaults. These are:

    SET PAGESIZE 2048
    SET CACHESIZE 200

The 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.

## Resources

dbxflat will ask you for the name of a resource definition in the file emboss.defaults. This will be something like:

    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.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

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

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None