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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 _ImgtScanner
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _ImgtScanner</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#_ImgtScanner">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html">InsdcScanner</a> --+
|
<a href="Bio.GenBank.Scanner.EmblScanner-class.html">EmblScanner</a> --+
|
<strong class="uidshort">_ImgtScanner</strong>
</pre>
<hr />
<p>For extracting chunks of information in IMGT (EMBL like) files
(PRIVATE).</p>
<p>IMGT files are like EMBL files but in order to allow longer feature
types the features should be indented by 25 characters not 21 characters.
In practice the IMGT flat files tend to use either 21 or 25 characters,
so we must cope with both.</p>
<p>This is private to encourage use of Bio.SeqIO rather than
Bio.GenBank.</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._ImgtScanner-class.html#parse_features" class="summary-sig-name">parse_features</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">skip</span>=<span class="summary-sig-default">False</span>)</span><br />
Return list of tuples for the features (if present)</td>
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<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#_ImgtScanner.parse_features">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank.Scanner.EmblScanner-class.html">EmblScanner</a></code></b>:
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#parse_footer">parse_footer</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank.Scanner.EmblScanner-class.html">EmblScanner</a></code></b> (private):
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_first_line" onclick="show_private();">_feed_first_line</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_first_line_new" onclick="show_private();">_feed_first_line_new</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_first_line_old" onclick="show_private();">_feed_first_line_old</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_header_lines" onclick="show_private();">_feed_header_lines</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_misc_lines" onclick="show_private();">_feed_misc_lines</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#_feed_seq_length" onclick="show_private();">_feed_seq_length</a></code>
</p></div>
<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_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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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.GenBank.Scanner._ImgtScanner-class.html#FEATURE_START_MARKERS" class="summary-name">FEATURE_START_MARKERS</a> = <code title="['FH Key Location/Qualifiers',
'FH Key Location/Qualifiers (from EMBL)',
'FH Key Location/Qualifiers',
'FH']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">FH Key Location/Qualif</code><code class="variable-ellipsis">...</code></code>
</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank.Scanner.EmblScanner-class.html">EmblScanner</a></code></b>:
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#FEATURE_END_MARKERS">FEATURE_END_MARKERS</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#FEATURE_QUALIFIER_INDENT">FEATURE_QUALIFIER_INDENT</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#FEATURE_QUALIFIER_SPACER">FEATURE_QUALIFIER_SPACER</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#HEADER_WIDTH">HEADER_WIDTH</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#RECORD_START">RECORD_START</a></code>,
<code><a href="Bio.GenBank.Scanner.EmblScanner-class.html#SEQUENCE_HEADERS">SEQUENCE_HEADERS</a></code>
</p>
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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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<a name="parse_features"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse_features</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">skip</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#_ImgtScanner.parse_features">source code</a></span>
</td>
</tr></table>
<p>Return list of tuples for the features (if present)</p>
<p>Each feature is returned as a tuple (key, location, qualifiers) where
key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers is
a list of two string tuples (feature qualifier keys and values).</p>
<p>Assumes you have already read to the start of the features table.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank.Scanner.InsdcScanner-class.html#parse_features">InsdcScanner.parse_features</a>
</dt>
</dl>
</td></tr></table>
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<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">FH Key Location/Qualifiers</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">FH Key Location/Qualifiers (from EMBL)</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">FH Key Location/Qualifiers</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">FH</code><code class="variable-quote">'</code><code class="variable-group">]</code>
</pre></td></tr></table>
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