|   | dbxcompress | 
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Indexes modified by dbxuncompress and indexes prior to EMBOSS 6.4.0 are uncompressed.
dbxcompress reads all pages, calculating the free space at the end of each page, and then rewrite the pages to disk removing all free space.
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.
Uncompressed index files are required for updating an existing index. Compressed index files provide more efficient storage and retrieval.
| % dbxcompress embl -indexdir . -field des Compress an uncompressed dbx index Output file [embl.dbxcompress]: | 
Go to the output files for this example
| 
Compress an uncompressed dbx index
Version: EMBOSS:6.6.0.0
   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    [*.dbxcompress] 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 | <*>.dbxcompress | 
| 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 | 
| Type Secondary Compress Yes Pages 21 Secpages 225 Order 22 Fill 21 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 223 Fullcount 445 Kwlimit 75 Idlimit 15 | 
This file contains non-printing characters and so cannot be displayed here.
| Compressing index 'des' for database 'embl' Index 'des' opened, compressing Completed | 
| 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 | 
| 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.