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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: dbxtax
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
dbxtax
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Index NCBI taxonomy using b+tree indices
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<!-- 
	This is the main part of the document.
        This is what the user looks at to find out if this program will do what he wants. 
        Long description.
        Why it is useful.
        When it should/shouldn't be used.
  -->

<b>dbxflat</b> indexes NCBI taxonomy files, and builds EMBOSS B+tree
format index files.

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



<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>dbxtax</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Index NCBI taxonomy using b+tree indices
Version: EMBOSS:6.6.0.0

   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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-dbname]<br>(Parameter 1)</td>
<td>string</td>
<td>Basename for index files</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td>taxon</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-dbresource]<br>(Parameter 2)</td>
<td>string</td>
<td>Resource name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td>taxresource</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-directory</td>
<td>directory</td>
<td>Database directory</td>
<td>Directory</td>
<td>.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-fields</td>
<td>list</td>
<td>Index fields</td>
<td><table><tr><td>id</td> <td><i>(ID)</i></td></tr><tr><td>acc</td> <td><i>(Synonym)</i></td></tr><tr><td>tax</td> <td><i>(Scientific name)</i></td></tr><tr><td>rnk</td> <td><i>(Rank)</i></td></tr><tr><td>up</td> <td><i>(Parent)</i></td></tr><tr><td>gc</td> <td><i>(Genetics code)</i></td></tr><tr><td>mgc</td> <td><i>(Mitochondrial genetic code)</i></td></tr></table></td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]compressed</td>
<td>boolean</td>
<td>Compressed index files</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>General log output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.dbxtax</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-release</td>
<td>string</td>
<td>Release number</td>
<td>Any string up to 9 characters</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-date</td>
<td>string</td>
<td>Index date</td>
<td>Date string dd/mm/yy</td>
<td>00/00/00</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-indexoutdir</td>
<td>outdir</td>
<td>Index file output directory</td>
<td>Output directory</td>
<td>.</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-directory" associated directory qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-indexoutdir" associated outdir qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<!-- 
        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
   -->

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

<p>






<H2>
    Output file format
</H2>

<!-- 
        This includes example output file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null output, errors etc. 

        If you wish to include the standard description of the avalable
	report formats, use:
        #include file="inc/reportformats.ihtml"
   -->

<b>dbxtax</b> creates one summary file for the database and two files
for each field indexed.

<p>

<ul>

<li>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.

<li>dbalias.xid is the B+tree index file for the ID names. It is a binary
file.

<li>dbalias.pxid is an ASCII file containing information regarding the
structure of the ID name index.


<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.dbxtax</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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'.
</pre>
</td></tr></table><p>
<p><h3>File: taxon.ent</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Reference 2 filename database
nodes.dmp names.dmp
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxac</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     0
Order        71
Fill         46
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        1
Fullcount    1
Kwlimit      15
Reffiles     1
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxgc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        3
Secpages     1
Order        132
Fill         65
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        1
Fullcount    41
Kwlimit      2
Idlimit      7
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxid</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     0
Order        99
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        41
Fullcount    41
Kwlimit      7
Reffiles     1
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxmgc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        3
Secpages     3
Order        132
Fill         65
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        3
Fullcount    39
Kwlimit      2
Idlimit      7
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxtax</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        14
Secpages     6
Order        14
Fill         13
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        86
Fullcount    90
Kwlimit      120
Reffiles     1
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxrnk</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        3
Secpages     17
Order        68
Fill         45
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        17
Fullcount    41
Kwlimit      16
Idlimit      7
</pre>
</td></tr></table><p>
<p><h3>File: taxon.pxup</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     12
Order        99
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        33
Fullcount    41
Kwlimit      7
Reffiles     1
</pre>
</td></tr></table><p>
<p><h3>File: taxon.xac</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xgc</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xid</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xmgc</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xrnk</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xtax</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: taxon.xup</h3>
<p>This file contains non-printing characters and so cannot be displayed here.





<H2>
    Data files
</H2>

<!-- 
        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.

	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:

        #include file="inc/localfiles.ihtml"
   -->

None.

<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="dbiblast.html">dbiblast</a></td>
<td>Index a BLAST database</td>
</tr>

<tr>
<td><a href="dbifasta.html">dbifasta</a></td>
<td>Index a fasta file database</td>
</tr>

<tr>
<td><a href="dbiflat.html">dbiflat</a></td>
<td>Index a flat file database</td>
</tr>

<tr>
<td><a href="dbigcg.html">dbigcg</a></td>
<td>Index a GCG formatted database</td>
</tr>

<tr>
<td><a href="dbxcompress.html">dbxcompress</a></td>
<td>Compress an uncompressed dbx index</td>
</tr>

<tr>
<td><a href="dbxedam.html">dbxedam</a></td>
<td>Index the EDAM ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxfasta.html">dbxfasta</a></td>
<td>Index a fasta file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxflat.html">dbxflat</a></td>
<td>Index a flat file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxgcg.html">dbxgcg</a></td>
<td>Index a GCG formatted database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxobo.html">dbxobo</a></td>
<td>Index an obo ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxreport.html">dbxreport</a></td>
<td>Validate index and report internals for dbx databases</td>
</tr>

<tr>
<td><a href="dbxresource.html">dbxresource</a></td>
<td>Index a data resource catalogue using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxstat.html">dbxstat</a></td>
<td>Dump statistics for dbx databases</td>
</tr>

<tr>
<td><a href="dbxuncompress.html">dbxuncompress</a></td>
<td>Uncompress a compressed dbx index</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>

Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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