                                  dbxreport



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Function

   Validate index and report internals for dbx databases

Description

   dbxreport reports statistics for the index fields of a database.

Algorithm

   The index directory is, by default, the index directory af an installed
   database.

   dbxreport reads the index file, reporting on the file name, the number
   of index terms, the depth of the index tree, statistics of internal
   page types and the free space in an uncompressed index.

Usage

   Here is a sample session with dbxreport


% dbxreport -indexdir .
Validate index and report internals for dbx databases
EMBOSS database name: embl
Index fields [id]: id,acc
Output file [embl.dbxreport]:


   Go to the output files for this example

Command line arguments

Validate index and report internals for dbx databases
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_]+/)
  [-fields]            string     [id] A list of index fields separated by
                                  spaces or commas. (Any string)
   -outfile            outfile    [*.dbxreport] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indexdir           directory  Index directory (optional)
   -fullreport         boolean    [N] Write full details to debug file

   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

   dbxreport reads index files created by any of the EMBOSS 'dbx' indexing
   applications.

Output file format

   The output is a text report of index statistics.

  Output files for usage example

  File: embl.dbxreport

Index 'id' (.xid)
  compressed:  Yes (Compressed)
   cachesize: 20000 (Size of primary cache)
seccachesize: 20000 (Size of secondary cache)
    pagesize: 2048 (Page size)
 secpagesize:  512 (Secondary page size)
   pagecount:    3 (Primary page count)
   pagecount:    0 (Secondary page count)
    refcount:    0 (Number of reference files)
       order:   71 (Tree order)
      sorder:   22 (Order of secondary tree)
       level:    0 (Level of tree)
      slevel:    0 (Level of secondary tree)
        fill:   56 (Entries per bucket)
       sfill:   41 (Entries per secondary bucket)
    keylimit:   15 (Max key size)
     idlimit:    0 (Max secondary id size)
       count:    6 (Unique entries in index)
   fullcount:    6 (Total entries in index)
Identifier index 'id' index found with 3 pages
      COUNT: 6
   COUNTALL: 6
       root: 1
     bucket: 2
...       keys: 1
...      bkeys: 6
...   total_size: 6144
...    freespace: 5871, 95.6% of uncompressed 6144
      FOUND: 6
   FOUNDALL: 6
Index 'acc' (.xac)
  compressed:  Yes (Compressed)
   cachesize: 20000 (Size of primary cache)
seccachesize: 20000 (Size of secondary cache)
    pagesize: 2048 (Page size)
 secpagesize:  512 (Secondary page size)
   pagecount:    3 (Primary page count)
   pagecount:    3 (Secondary page count)
    refcount:    0 (Number of reference files)
       order:   71 (Tree order)
      sorder:   22 (Order of secondary tree)
       level:    0 (Level of tree)
      slevel:    0 (Level of secondary tree)
        fill:   56 (Entries per bucket)
       sfill:   41 (Entries per secondary bucket)
    keylimit:   15 (Max key size)
     idlimit:    0 (Max secondary id size)
       count:    7 (Unique entries in index)
   fullcount:    9 (Total entries in index)
Identifier index 'acc' index found with 6 pages
      COUNT: 7
   COUNTALL: 9
       root: 1
    numroot: 1
     bucket: 2
  numbucket: 2
...       keys: 2
...      bkeys: 7
...      bdups: 1
...      bxtra: 2
...      nkeys: 3 (0)
...   total_size: 7680
...    freespace: 7236, 94.2% of uncompressed 7680
      FOUND: 7
   FOUNDALL: 9

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
                    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 everyone and everything, from
                    naive users to embedded scripts.

Comments

                    None
