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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">
object --+
|
<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 />
Scan over and parse GenBank LOCUS line (PRIVATE).</td>
<td align="right" valign="top">
<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>
</td>
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</td>
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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>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
</td><td class="summary">
<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>
</td>
</tr>
<tr>
<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>
</tr>
<tr>
<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>
</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<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>
</tr>
<tr>
<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>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<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', 'WGS']"><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-op">, </code><code class="variable-quote">'</code><code class="variable-string">WGS</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="parse_footer"></a>
<div>
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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">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">
<tr valign="top"><td>
<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>Scan over and parse GenBank LOCUS line (PRIVATE).</p>
<p>This must cope with several variants, primarily the old and new column
based standards from GenBank. Additionally EnsEMBL produces GenBank files
where the LOCUS line is space separated rather that following the column
based layout.</p>
<p>We also try to cope with GenBank like files with partial LOCUS
lines.</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>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_feed_header_lines"></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">
<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">
<table class="details" border="1" cellpadding="3"
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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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<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>
</pre></td></tr></table>
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