                                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


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 (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
