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EMBOSS: dbxcompress
dbxcompress

 

Wiki

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Function

Compress an uncompressed dbx index

Description

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

Indexes modified by dbxuncompress and indexes prior to EMBOSS 6.4.0 are uncompressed.

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, 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.

Usage

Here is a sample session with dbxcompress 


% dbxcompress embl -indexdir . -field des 
Compress an uncompressed dbx index
Output file [embl.dbxcompress]:

Go to the output files for this example

Command line arguments 

Compress an uncompressed dbx index
Version: EMBOSS:6.4.0.0

   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

Input file format

dbxcompress reads the index files for a database created with an older version of one of the 'dbx' indexing programs, or uncompressed with dbxuncompress.

Output file format

dbxcompress rewrites the index files in compressed form.

Output files for usage example

File: embl.pxde

Type      Secondary
Compress  Yes
Pages     647
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     213
Fullcount 417
Kwlimit   20

File: embl.xde

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

File: embl.dbxcompress

Compressing index 'des' for database 'embl'
Index 'des' opened, compressing
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
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

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