EMBOSS: dbxtax

| dbxtax

## 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

Index NCBI taxonomy using b+tree indices

## Description

dbxflat indexes NCBI taxonomy files, and builds EMBOSS B+tree format index files.

These indexes allow access of flat files larger than 2Gb.

## Usage

Here is a sample session with dbxtax

    % dbxtax
    Index NCBI taxonomy using b+tree indices
    Basename for index files [taxon]:
    Resource name [taxresource]:
    Database directory [.]: taxonomy
            id : ID
           acc : Synonym
           tax : Scientific name
           rnk : Rank
            up : Parent
            gc : Genetics code
           mgc : Mitochondrial genetic code
    Index fields [*]:
    Compressed index files [Y]:
    General log output file [outfile.dbxtax]:

Go to the output files for this example

## Command line arguments

    Index NCBI taxonomy using b+tree indices
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-dbname]            string     [taxon] Basename for index files (Any string
                                      from 2 to 19 characters, matching regular
                                      expression /[A-z][A-z0-9_]+/)
      [-dbresource]        string     [taxresource] Resource name (Any string from
                                      2 to 19 characters, matching regular
                                      expression /[A-z][A-z0-9_]+/)
       -directory          directory  [.] Database directory
       -fields             menu       [*] Index fields (Values: id (ID); acc
                                      (Synonym); tax (Scientific name); rnk
                                      (Rank); up (Parent); gc (Genetics code); mgc
                                      (Mitochondrial genetic code))
       -[no]compressed     boolean    [Y] Compressed index files
       -outfile            outfile    [*.dbxtax] General log output file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -release            string     [0.0] Release number (Any string up to 9
                                      characters)
       -date               string     [00/00/00] Index date (Date string dd/mm/yy)
       -indexoutdir        outdir     [.] Index file output directory

       Associated qualifiers:

       "-directory" associated qualifiers
       -extension          string     Default file extension

       "-indexoutdir" 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 | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | taxon
[-dbresource] (Parameter 2) | string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | taxresource
-directory | directory | Database directory | Directory | .
-fields | list | Index fields |
id | (ID)
acc | (Synonym)
tax | (Scientific name)
rnk | (Rank)
up | (Parent)
gc | (Genetics code)
mgc | (Mitochondrial genetic code)
| *
-[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes
-outfile | outfile | General log output file | Output file | <*>.dbxtax
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-release | string | Release number | Any string up to 9 characters | 0.0
-date | string | Index date | Date string dd/mm/yy | 00/00/00
-indexoutdir | outdir | Index file output directory | Output directory | .
Associated qualifiers
"-directory" associated directory qualifiers
-extension | string | Default file extension | Any string |
"-indexoutdir" associated outdir 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

dbxtax reads and indexes the NCBI taxonomy nodes.dmp, names.dmp, division.dmp, gencode.dmp,and merged.dmp files.

## Output file format

dbxtax creates one summary file for the database and two files for each field indexed.

- dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
- dbalias.xid is the B+tree index file for the ID names. It is a binary file.
- dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

  ### Output files for usage example

  ### File: outfile.dbxtax

      Processing directory: /homes/user/test/data/taxonomy/
      Processing file: nodes.dmp
      entries: 41 (41) time: 0.0s (0.0s)
      Total time: 0.0s
      Entry idlen 7 OK. Maximum ID length was 6 for '117570'.
      Field acc acclen 15 OK. Maximum acc term length was 5 for '40673'.
      Field tax taxlen 120 OK. Maximum tax term length was 23 for 'Pongo abelii x pygmaeus'.
      Field rnk rnklen 16 OK. Maximum rnk term length was 12 for 'superkingdom'.
      Field up uplen 7 OK. Maximum up term length was 6 for '131567'.
      Field gc gclen 2 OK. Maximum gc term length was 1 for '1'.
      Field mgc mgclen 2 OK. Maximum mgc term length was 1 for '1'.

  ### File: taxon.ent

      # Number of files: 1
      # Release: 0.0
      # Date:    00/00/00
      Reference 2 filename database
      nodes.dmp names.dmp

  ### File: taxon.pxac

      Type         Identifier
      Compress     Yes
      Pages        3
      Secpages     0
      Order        71
      Fill         46
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        24
      Secpagesize  512
      Seccachesize 2000
      Count        1
      Fullcount    1
      Kwlimit      15
      Reffiles     1

  ### File: taxon.pxgc

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     1
      Order        132
      Fill         65
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        41
      Secpagesize  512
      Seccachesize 2000
      Count        1
      Fullcount    41
      Kwlimit      2
      Idlimit      7

  ### File: taxon.pxid

      Type         Identifier
      Compress     Yes
      Pages        3
      Secpages     0
      Order        99
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        24
      Secpagesize  512
      Seccachesize 2000
      Count        41
      Fullcount    41
      Kwlimit      7
      Reffiles     1

  ### File: taxon.pxmgc

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     3
      Order        132
      Fill         65
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        41
      Secpagesize  512
      Seccachesize 2000
      Count        3
      Fullcount    39
      Kwlimit      2
      Idlimit      7

  ### File: taxon.pxtax

      Type         Identifier
      Compress     Yes
      Pages        14
      Secpages     6
      Order        14
      Fill         13
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        24
      Secpagesize  512
      Seccachesize 2000
      Count        86
      Fullcount    90
      Kwlimit      120
      Reffiles     1

  ### File: taxon.pxrnk

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     17
      Order        68
      Fill         45
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        41
      Secpagesize  512
      Seccachesize 2000
      Count        17
      Fullcount    41
      Kwlimit      16
      Idlimit      7

  ### File: taxon.pxup

      Type         Identifier
      Compress     Yes
      Pages        3
      Secpages     12
      Order        99
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        24
      Secpagesize  512
      Seccachesize 2000
      Count        33
      Fullcount    41
      Kwlimit      7
      Reffiles     1

  ### File: taxon.xac

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

  ### File: taxon.xgc

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

  ### File: taxon.xid

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

  ### File: taxon.xmgc

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

  ### File: taxon.xrnk

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

  ### File: taxon.xtax

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

  ### File: taxon.xup

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

  ## 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
  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