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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.config-module.html">Package config</a> ::
Module SeqDBRegistry
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module SeqDBRegistry</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html">source code</a></span></p>
<p>This module handles seqdatabase.INI file.</p>
<p>Classes: SeqDBRegistry Holds databases from seqdatabase.INI.</p>
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<span class="summary-type"> </span>
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<a href="Bio.config.SeqDBRegistry.SeqDBRegistry-class.html" class="summary-name">SeqDBRegistry</a><br />
This object implements a dictionary-like interface to sequence
databases.
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<td><span class="summary-sig"><a name="_warn"></a><span class="summary-sig-name">_warn</span>(<span class="summary-sig-arg">message</span>)</span></td>
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<span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html#_warn">source code</a></span>
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<td><span class="summary-sig"><a name="_load_registry_objects"></a><span class="summary-sig-name">_load_registry_objects</span>(<span class="summary-sig-arg">ini_file</span>)</span></td>
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<span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html#_load_registry_objects">source code</a></span>
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<td><span class="summary-sig"><a name="_make_biofetch_db"></a><span class="summary-sig-name">_make_biofetch_db</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">tagvalue_dict</span>)</span></td>
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<td><span class="summary-sig"><a name="_make_biosql_db"></a><span class="summary-sig-name">_make_biosql_db</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">tagvalue_dict</span>)</span><br />
Register a BioSQL database defined in the registry.</td>
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<td><span class="summary-sig"><a name="_make_flat_db"></a><span class="summary-sig-name">_make_flat_db</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">tagvalue_dict</span>)</span><br />
Register a Berkeley or Flat indexed file defined in the registry.</td>
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<span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html#_make_flat_db">source code</a></span>
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Guess whether this is a file or url and open it.</td>
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<span class="summary-type">list of URL's or paths to search for files</span>
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<td><span class="summary-sig"><a href="Bio.config.SeqDBRegistry-module.html#_list_ini_paths" class="summary-sig-name" onclick="show_private();">_list_ini_paths</a>()</span><br />
The default places to look for registry files are:</td>
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<span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html#_list_ini_paths">source code</a></span>
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<span class="summary-type">list of files to search (in order)</span>
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<td><span class="summary-sig"><a name="_list_ini_files"></a><span class="summary-sig-name">_list_ini_files</span>(<span class="summary-sig-arg">filename</span>)</span></td>
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<span class="codelink"><a href="Bio.config.SeqDBRegistry-pysrc.html#_list_ini_files">source code</a></span>
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<a name="seqdb"></a><span class="summary-name">seqdb</span> = <code title="seqdb">seqdb</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_list_ini_paths</span>()</span>
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<p>The default places to look for registry files are:</p>
<ul>
<li>
${HOME}/.bioinformatics
</li>
<li>
/etc/bioinformatics
</li>
<li>
http://www.open-bio.org/registry
<p>The OBDA_SEARCH_PATH environment variable, if specified, overrides
the default. This should be a "+" separated list of paths
or URL's.</p>
</li>
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<dt>Returns: list of URL's or paths to search for files</dt>
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