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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GenBank-module.html">Package GenBank</a> ::
<a href="Bio.GenBank.Scanner-module.html">Module Scanner</a> ::
Class GenBankScanner
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class GenBankScanner</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html">InsdcScanner</a> --+
|
<strong class="uidshort">GenBankScanner</strong>
</pre>
<hr />
<p>For extracting chunks of information in GenBank files</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Scanner.GenBankScanner-class.html#parse_footer" class="summary-sig-name">parse_footer</a>(<span class="summary-sig-arg">self</span>)</span><br />
returns a tuple containing a list of any misc strings, and the
sequence</td>
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<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner.parse_footer">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Scanner.GenBankScanner-class.html#_feed_first_line" class="summary-sig-name" onclick="show_private();">_feed_first_line</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">line</span>)</span><br />
Handle the LOCUS/ID line, passing data to the comsumer</td>
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<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_first_line">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Scanner.GenBankScanner-class.html#_feed_header_lines" class="summary-sig-name" onclick="show_private();">_feed_header_lines</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">lines</span>)</span><br />
Handle the header lines (list of strings), passing data to the
comsumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_header_lines">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Scanner.GenBankScanner-class.html#_feed_misc_lines" class="summary-sig-name" onclick="show_private();">_feed_misc_lines</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">lines</span>)</span><br />
Handle any lines between features and sequence (list of strings),
passing data to the consumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_misc_lines">source code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html">InsdcScanner</a></code></b>:
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#__init__">__init__</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#feed">feed</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#find_start">find_start</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse">parse</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_cds_features">parse_cds_features</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_feature">parse_feature</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_features">parse_features</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_header">parse_header</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_records">parse_records</a></code>,
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#set_handle">set_handle</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html">InsdcScanner</a></code></b> (private):
<code><a href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_feature_table" onclick="show_private();">_feed_feature_table</a></code>
</p></div>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
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<a name="RECORD_START"></a><span class="summary-name">RECORD_START</span> = <code title="'LOCUS '"><code class="variable-quote">'</code><code class="variable-string">LOCUS </code><code class="variable-quote">'</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="HEADER_WIDTH"></a><span class="summary-name">HEADER_WIDTH</span> = <code title="12">12</code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.GenBank.Scanner.GenBankScanner-class.html#FEATURE_START_MARKERS" class="summary-name">FEATURE_START_MARKERS</a> = <code title="['FEATURES Location/Qualifiers', 'FEATURES']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">FEATURES Location/Qualif</code><code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_END_MARKERS"></a><span class="summary-name">FEATURE_END_MARKERS</span> = <code title="[]"><code class="variable-group">[</code><code class="variable-group">]</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_QUALIFIER_INDENT"></a><span class="summary-name">FEATURE_QUALIFIER_INDENT</span> = <code title="21">21</code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_QUALIFIER_SPACER"></a><span class="summary-name">FEATURE_QUALIFIER_SPACER</span> = <code title="' '"><code class="variable-quote">'</code><code class="variable-string"> </code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="SEQUENCE_HEADERS"></a><span class="summary-name">SEQUENCE_HEADERS</span> = <code title="['CONTIG', 'ORIGIN', 'BASE COUNT']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">CONTIG</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ORIGIN</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">BASE COUNT</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<!-- ==================== METHOD DETAILS ==================== -->
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>hide private</a>]</span></td>
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<a name="parse_footer"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse_footer</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner.parse_footer">source code</a></span>
</td>
</tr></table>
<p>returns a tuple containing a list of any misc strings, and the
sequence</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_footer">InsdcScanner.parse_footer</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_feed_first_line"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_feed_first_line</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">line</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_first_line">source code</a></span>
</td>
</tr></table>
<p>Handle the LOCUS/ID line, passing data to the comsumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_first_line" onclick="show_private();">InsdcScanner._feed_first_line</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_feed_header_lines"></a>
<div class="private">
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_feed_header_lines</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_header_lines">source code</a></span>
</td>
</tr></table>
<p>Handle the header lines (list of strings), passing data to the
comsumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_header_lines" onclick="show_private();">InsdcScanner._feed_header_lines</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_feed_misc_lines"></a>
<div class="private">
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_feed_misc_lines</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#GenBankScanner._feed_misc_lines">source code</a></span>
</td>
</tr></table>
<p>Handle any lines between features and sequence (list of strings),
passing data to the consumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_misc_lines" onclick="show_private();">InsdcScanner._feed_misc_lines</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<br />
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<a name="FEATURE_START_MARKERS"></a>
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<h3 class="epydoc">FEATURE_START_MARKERS</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">FEATURES Location/Qualifiers</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">FEATURES</code><code class="variable-quote">'</code><code class="variable-group">]</code>
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