EMBOSS: dbxstat

| dbxstat

## 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

Dump statistics for dbx databases

## Description

dbxstat reports the contents of a B+ tree database index.

## Usage

Here is a sample session with dbxstat

    % dbxstat
    Dump statistics for dbx databases
    EMBOSS database name: edam
    EMBOSS database field [id]: ns
    Output file [edam.dbxstat]:

Go to the output files for this example

## Command line arguments

    Dump statistics for dbx databases
    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     [id] EMBOSS database field (Any string)
       -outfile            outfile    [*.dbxstat] Output file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -indexdir           directory  Index directory (optional)
       -minimum            integer    [1] Minimum occurrences (Integer 1 or more)
       -maximum            integer    [0] Maximum occurrences (0=no maximum)
                                      (Integer 0 or more)

       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 | id
-outfile | outfile | Output file name | Output file | <*>.dbxstat
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-indexdir | directory | Index directory (optional) | Directory |
-minimum | integer | Minimum occurrences | Integer 1 or more | 1
-maximum | integer | Maximum occurrences (0=no maximum) | Integer 0 or more | 0
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

dbxstat reads the index files for any database defined with "emboss" access method.

## Output file format

dbxstat reports the contents of the selected index files.

### Output files for usage example

### File: edam.dbxstat

           819 data
           435 format
           605 identifier
           614 operation
           245 topic

    Total keywords: 5 IDs: 2718

## 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
dbxtax | Index NCBI taxonomy using b+tree indices
dbxuncompress | Uncompress a compressed dbx index

## Author(s)

Alan Bleasby
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 everyone and everything, from naive users to embedded scripts.

## Comments

None