dbxcompress



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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


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 (c) 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