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Bio ::
GenBank ::
_BaseGenBankConsumer ::
Class _BaseGenBankConsumer
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _BaseGenBankConsumer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a> --+
|
<strong class="uidshort">_BaseGenBankConsumer</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.GenBank._FeatureConsumer-class.html">_FeatureConsumer</a></li><li>, <a href="Bio.GenBank._RecordConsumer-class.html">_RecordConsumer</a></li> </ul>
</dd></dl>
<hr />
<p>Abstract GenBank consumer providing useful general functions.</p>
<p>This just helps to eliminate some duplication in things that most
GenBank consumers want to do.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="_split_keywords"></a><span class="summary-sig-name">_split_keywords</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">keyword_string</span>)</span><br />
Split a string of keywords into a nice clean list.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._split_keywords">source code</a></span>
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<td><span class="summary-sig"><a name="_split_accessions"></a><span class="summary-sig-name">_split_accessions</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">accession_string</span>)</span><br />
Split a string of accession numbers into a list.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._split_accessions">source code</a></span>
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<td><span class="summary-sig"><a name="_split_taxonomy"></a><span class="summary-sig-name">_split_taxonomy</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxonomy_string</span>)</span><br />
Split a string with taxonomy info into a list.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._split_taxonomy">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_clean_location" class="summary-sig-name" onclick="show_private();">_clean_location</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">location_string</span>)</span><br />
Clean whitespace out of a location string.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._clean_location">source code</a></span>
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<td><span class="summary-sig"><a name="_remove_newlines"></a><span class="summary-sig-name">_remove_newlines</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>)</span><br />
Remove any newlines in the passed text, returning the new string.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._remove_newlines">source code</a></span>
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<td><span class="summary-sig"><a name="_normalize_spaces"></a><span class="summary-sig-name">_normalize_spaces</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>)</span><br />
Replace multiple spaces in the passed text with single spaces.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._normalize_spaces">source code</a></span>
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<td><span class="summary-sig"><a name="_remove_spaces"></a><span class="summary-sig-name">_remove_spaces</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>)</span><br />
Remove all spaces from the passed text.</td>
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<td><span class="summary-sig"><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_convert_to_python_numbers" class="summary-sig-name" onclick="show_private();">_convert_to_python_numbers</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>)</span><br />
Convert a start and end range to python notation.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._convert_to_python_numbers">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a></code></b>:
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#__getattr__">__getattr__</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a></code></b> (private):
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled" onclick="show_private();">_unhandled</a></code>,
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled_section" onclick="show_private();">_unhandled_section</a></code>
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<a name="remove_space_keys"></a><span class="summary-name">remove_space_keys</span> = <code title="['translation']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">translation</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_clean_location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">location_string</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._clean_location">source code</a></span>
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<p>Clean whitespace out of a location string.</p>
<p>The location parser isn't a fan of whitespace, so we clean it out
before feeding it into the parser.</p>
<dl class="fields">
</dl>
</td></tr></table>
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<a name="_convert_to_python_numbers"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_convert_to_python_numbers</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">start</span>,
<span class="sig-arg">end</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_BaseGenBankConsumer._convert_to_python_numbers">source code</a></span>
</td>
</tr></table>
<p>Convert a start and end range to python notation.</p>
<p>In GenBank, starts and ends are defined in "biological"
coordinates, where 1 is the first base and [i, j] means to include both i
and j.</p>
<p>In python, 0 is the first base and [i, j] means to include i, but not
j.</p>
<p>So, to convert "biological" to python coordinates, we need
to subtract 1 from the start, and leave the end and things should be
converted happily.</p>
<dl class="fields">
</dl>
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