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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: dbxobo
  </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">
dbxobo
</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 an obo ontology using b+tree indices
<H2>
    Description
</H2>

<b>dbxobo</b> indexes an ontology in OBO format, and builds
EMBOSS B+tree format index files.

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

<p>
Related application <b>dbxedam</b> provides additional index fields
for EDAM-specific namespaces and relations.


<H2>
    Usage
</H2>
Here is a sample session with <b>dbxobo</b>
<p>

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

% <b>dbxobo </b>
Index an obo ontology using b+tree indices
Basename for index files: <b>edam</b>
Standard database name [edam]: <b></b>
Resource name [oboresource]: <b>oboresource</b>
Database directory [.]: <b></b>
Wildcard database filename [*.obo]: <b>EDAM.obo</b>
        id : ID
       acc : Synonym
       nam : Name
       isa : Parent
       des : Description
        ns : Namespace
Index fields [*]: <b>*</b>
Compressed index files [Y]: <b></b>
General log output file [outfile.dbxobo]: <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 an obo ontology 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_]+/)
  [-standardname]      string     [$(dbname)] Standard database name (Any
                                  string from 2 to 19 characters, matching
                                  regular expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     [oboresource] Resource name (Any string from
                                  2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [*.obo] Wildcard database filename (Any
                                  string)
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (Synonym); nam (Name); isa (Parent); des
                                  (Description); ns (Namespace))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxobo] 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)
   -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>[-standardname]<br>(Parameter 2)</td>
<td>string</td>
<td>Standard database name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td>$(dbname)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-dbresource]<br>(Parameter 3)</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>oboresource</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>-filenames</td>
<td>string</td>
<td>Wildcard database filename</td>
<td>Any string</td>
<td>*.obo</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>nam</td> <td><i>(Name)</i></td></tr><tr><td>isa</td> <td><i>(Parent)</i></td></tr><tr><td>des</td> <td><i>(Description)</i></td></tr><tr><td>ns</td> <td><i>(Namespace)</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>.dbxobo</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>-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>

<H2>
    Input file format
</H2>

<b>dbxobo</b> reads and indexes OBO format ontology files

<p>


<H2>
    Output file format
</H2>

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

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.dbxobo</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Processing directory: /homes/user/test/data/
Processing file: EDAM.obo
entries: 143 (143) time: 0.0s (0.0s)
Total time: 0.0s
Entry idlen 15 OK. Maximum ID length was 4 for '0004'.
Field acc acclen 200 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'.
Field nam namlen 70 OK. Maximum nam term length was 15 for 'semanticscience'.
Field isa isalen 15 OK. Maximum isa term length was 4 for '0003'.
Field ns nslen 20 OK. Maximum ns term length was 10 for 'identifier'.
Field des deslen 50 OK. Maximum des term length was 17 for 'conceptualisation'.
</pre>
</td></tr></table><p>
<p><h3>File: edam.ent</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
EDAM.obo
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxac</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        3
Secpages     0
Order        76
Fill         74
Level        0
Pagesize     16384
Cachesize    20000
Order2       816
Fill2        1364
Secpagesize  16384
Seccachesize 20000
Count        143
Fullcount    143
Kwlimit      200
Reffiles     0
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxde</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        21
Secpages     562
Order        64
Fill         57
Level        0
Pagesize     4096
Cachesize    20000
Order2       144
Fill2        204
Secpagesize  4096
Seccachesize 20000
Count        562
Fullcount    2167
Kwlimit      50
Idlimit      15
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxid</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Identifier
Compress     Yes
Pages        5
Secpages     0
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        143
Fullcount    143
Kwlimit      15
Reffiles     0
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxis</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        4
Secpages     96
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        90
Fullcount    225
Kwlimit      15
Idlimit      15
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxnm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        5
Secpages     323
Order        196
Fill         179
Level        0
Pagesize     16384
Cachesize    20000
Order2       583
Fill2        818
Secpagesize  16384
Seccachesize 20000
Count        323
Fullcount    725
Kwlimit      70
Idlimit      15
</pre>
</td></tr></table><p>
<p><h3>File: edam.pxns</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        3
Secpages     12
Order        60
Fill         49
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        5
Fullcount    143
Kwlimit      20
Idlimit      15
</pre>
</td></tr></table><p>
<p><h3>File: edam.xac</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: edam.xde</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: edam.xid</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: edam.xis</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: edam.xnm</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: edam.xns</h3>
<p>This file contains non-printing characters and so cannot be displayed here.

<H2>
    Data files
</H2>

        
<H2>
    Notes
</H2>



<H2>
    References
</H2>

  

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.


<H2>
    Exit status
</H2>

It exits with a status of 0.

<H2>
    Known bugs
</H2>

None.

<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="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>

<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>



<H2>
    Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 

<H2>
    Comments
</H2>
None

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