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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: dbxflat
  </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">
dbxflat
</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 a flat file database 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 a flat file database of one or more 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>dbxflat</b>
<p>

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

% <b>dbxflat </b>
Index a flat file database using b+tree indices
Basename for index files: <b>embl</b>
Resource name: <b>emblresource</b>
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
     FASTQ : Fastq files
     USPTO : Iguspto files
Entry format [SWISS]: <b>embl</b>
Wildcard database filename [*.dat]: <b>rod.dat</b>
Database directory [.]: <b>embl</b>
        id : ID
       acc : Accession number
        sv : Sequence Version and GI
       des : Description
       key : Keywords
       org : Taxonomy
Index fields [id,acc]: <b></b>
Compressed index files [Y]: <b></b>
General log output file [outfile.dbxflat]: <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 a flat file database using b+tree indices
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Basename for index files (Any string from 2
                                  to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     Resource name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [SWISS] Entry format (Values: EMBL (EMBL);
                                  SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); GB
                                  (Genbank, DDBJ); REFSEQ (Refseq); FASTQ
                                  (Fastq files); USPTO (Iguspto files))
   -filenames          string     [*.dat] Wildcard database filename (Any
                                  string)
   -directory          directory  [.] Database directory
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description); key (Keywords); org
                                  (Taxonomy))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxflat] 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)
   -exclude            string     Wildcard filename(s) to exclude (Any string)
   -statistics         boolean    [N] Report I/O statistics for each input
                                  file
   -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><b>Required</b></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><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-idformat</td>
<td>list</td>
<td>Entry format</td>
<td><table><tr><td>EMBL</td> <td><i>(EMBL)</i></td></tr><tr><td>SWISS</td> <td><i>(Swiss-Prot, SpTrEMBL, TrEMBLnew)</i></td></tr><tr><td>GB</td> <td><i>(Genbank, DDBJ)</i></td></tr><tr><td>REFSEQ</td> <td><i>(Refseq)</i></td></tr><tr><td>FASTQ</td> <td><i>(Fastq files)</i></td></tr><tr><td>USPTO</td> <td><i>(Iguspto files)</i></td></tr></table></td>
<td>SWISS</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-filenames</td>
<td>string</td>
<td>Wildcard database filename</td>
<td>Any string</td>
<td>*.dat</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>(Accession number)</i></td></tr><tr><td>sv</td> <td><i>(Sequence Version and GI)</i></td></tr><tr><td>des</td> <td><i>(Description)</i></td></tr><tr><td>key</td> <td><i>(Keywords)</i></td></tr><tr><td>org</td> <td><i>(Taxonomy)</i></td></tr></table></td>
<td>id,acc</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>.dbxflat</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>-exclude</td>
<td>string</td>
<td>Wildcard filename(s) to exclude</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-statistics</td>
<td>boolean</td>
<td>Report I/O statistics for each input file</td>
<td>Boolean value Yes/No</td>
<td>No</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>dbxflat</b> reads and indexes sequence data flatfiles in any of the available
formats.

<p>






<H2>
    Output file format
</H2>


<b>dbxflat</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.

</ul>


<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.dbxflat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Processing directory: /homes/user/test/embl/
Processing file: rod.dat
entries: 6 (6) time: 0.0/0.0s (0.0/0.0s)
Total time: 0:00.0
Entry idlen 15 OK. Maximum ID length was 6 for 'L48662'.
Field acc acclen 15 OK. Maximum acc term length was 6 for 'L48662'.
</pre>
</td></tr></table><p>
<p><h3>File: embl.ent</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
rod.dat
</pre>
</td></tr></table><p>
<p><h3>File: embl.pxac</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     3
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        7
Fullcount    9
Kwlimit      15
Reffiles     0
</pre>
</td></tr></table><p>
<p><h3>File: embl.pxid</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     0
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        6
Fullcount    6
Kwlimit      15
Reffiles     0
</pre>
</td></tr></table><p>
<p><h3>File: embl.xac</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: embl.xid</h3>
<p>This file contains non-printing characters and so cannot be displayed here.





<H2>
    Data files
</H2>


None.











<H2>
    Notes
</H2>

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

The indexing system has been designed to allow on-the-fly updating
of indexes. This feature is, however, not implemented in the current
version. It will be made available in future releases.



<p>

Having created the EMBOSS indexes for this file, a database can then be
defined in the file <b>emboss.defaults</b> as something like:

<pre>
DB embl [
   type: N
   dbalias: embl   (see below)
   format: embl
   method: emboss
   directory: /data/embl
   file: *.dat
   indexdirectory: /data/embl/indexes
]
</pre>

The index file 'basename' given to <b>dbxflat</b> must match the DB name
in the definition. If not, then a 'dbalias' line must be given which
specifies the basename of the indexes. 

<h3>Fields Indexed</H3>

By default, <b>dbxflat</b> will index the ID name and the accession
number (if present).

<br>

If they are present in your database, you may also specify that
<b>dbxflat</b> should index the Sequence Version and GI, the words
in the description, the keywords and the organism words using the
'-fields' qualifier with the appropriate values.   





<H2>
    Global Parameters
</H2>

<b>dbxflat</b> requires that two global parameters be defined in
the file <b>emboss.defaults</b>. These are:

<pre>
SET PAGESIZE 2048
SET CACHESIZE 200
</pre>

The above values are recommended for most systems. The PAGESIZE is
a multiple of the size of disc pages the operating system buffers.
The CACHESIZE is the number of disc pages <b>dbxflat</b> is
allowed to cache.


<H2>
    Resources
</H2>


<b>dbxflat</b> will ask you for the name of a resource definition
in the file <b>emboss.defaults</b>. This will be something like:

<pre>
RES embl [
   type: Index
   idlen:  15
   acclen: 15
   svlen:  20
   keylen: 25
   deslen: 25
   orglen: 25
]
</pre>

The length definitions are the maximum lengths of 'words' in the
field being indexed. Longer words will be truncated to the
value set.








<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="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="dbxtax.html">dbxtax</a></td>
<td>Index NCBI taxonomy using b+tree indices</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>

Alan Bleasby 
<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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