EMBOSS: dbxuncompress

| dbxuncompress

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Uncompress a compressed dbx index

## Description

dbxuncompress uncompresses EMBOSS B+tree format index files. By default, the indexing applications in EMBOSS compress all index files.

Indexes prior to EMBOSS 6.4.0 are uncompressed.

Uncompressed index files are required for updating an existing index. Compressed index files provide more efficient storage and retrieval.

## Algorithm

The B+tree index files contain discrete pages with a known maximum size, filled from the first byte with a count of index terms.

dbxcompress reads all pages, identifying the end of the used space and adding calculating the free space at the end of each page and calculating the new start position for each uncompressed page. It then rereads the index file, and rewrites the pages to disk expanded to the full page size.

The final page is always written in full. This allows index reading to assume the maximum page size in all cases without reading beyond the end of file.

## Usage

Here is a sample session with dbxuncompress

    % dbxuncompress embl -indexdir . -field des
    Uncompress a compressed dbx index
    Output file [embl.dbxuncompress]:

Go to the output files for this example

## Command line arguments

    Uncompress a compressed dbx index
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-dbname]            string     EMBOSS database name (Any string from 2 to
                                      19 characters, matching regular expression
                                      /[A-z][A-z0-9_]+/)
      [-field]             string     EMBOSS database field (Any string)
       -outfile            outfile    [*.dbxuncompress] Output file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -indexdir           directory  Index directory (optional)

       Associated qualifiers:

       "-indexdir" associated qualifiers
       -extension          string     Default file extension

       "-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 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 | EMBOSS database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required
[-field] (Parameter 2) | string | EMBOSS database field | Any string |
-outfile | outfile | Output file name | Output file | <*>.dbxuncompress
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-indexdir | directory | Index directory (optional) | Directory |
Associated qualifiers
"-indexdir" associated directory qualifiers
-extension | string | Default file extension | Any string |
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | 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

## Input file format

dbxuncompress reads the index files for a database created with one of the 'dbx' indexing programs.

## Output file format

dbxuncompress rewrites the index files in uncompressed form.

### Output files for usage example

### File: embl.pxde

    Type         Secondary
    Compress     No
    Pages        21
    Secpages     225
    Order        22
    Fill         21
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        223
    Fullcount    445
    Kwlimit      75
    Idlimit      15

### File: embl.xde

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

### File: embl.dbxuncompress

    Uncompressing index 'des' for database 'embl'
    Index 'des' uncompressed
    Completed

## Data files

None.

## Notes

None.

## 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
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

## Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

## Comments

None