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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Prosite-module.html">Package Prosite</a> ::
<a href="Bio.Prosite.Pattern-module.html">Module Pattern</a> ::
Class PrositeMatch
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PrositeMatch</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#PrositeMatch">source code</a></span></p>
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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 class="summary-sig-arg">prosite</span>,
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<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="__getslice__"></a><span class="summary-sig-name">__getslice__</span>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a href="Bio.Prosite.Pattern.PrositeMatch-class.html#mapping" class="summary-sig-name">mapping</a>(<span class="summary-sig-arg">self</span>)</span><br />
return a list of numbers mapping to items of the original pattern</td>
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<td><span class="summary-sig"><a href="Bio.Prosite.Pattern.PrositeMatch-class.html#mapped_pattern" class="summary-sig-name">mapped_pattern</a>(<span class="summary-sig-arg">self</span>)</span><br />
returns the specific Prosite pattern used to find this sequence</td>
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<td><span class="summary-sig"><a name="start"></a><span class="summary-sig-name">start</span>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a name="end"></a><span class="summary-sig-name">end</span>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a name="span"></a><span class="summary-sig-name">span</span>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a name="groups"></a><span class="summary-sig-name">groups</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">default</span>=<span class="summary-sig-default">None</span>)</span></td>
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<td><span class="summary-sig"><a name="group"></a><span class="summary-sig-name">group</span>(<span class="summary-sig-arg">self</span>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">mapping</span>(<span class="sig-arg">self</span>)</span>
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<p>return a list of numbers mapping to items of the original pattern</p>
<p>For example, if the Prosite pattern is "[AP](2)-D." matched
against "PAD", then the mapping is [1, 1, 2], meaning the first
character of the match ("P") is from the first Prosite group
("[AP]"), as is the second letter ("A"). The 3rd
letter ("D") is mapped to group 2 of the pattern.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">mapped_pattern</span>(<span class="sig-arg">self</span>)</span>
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<p>returns the specific Prosite pattern used to find this sequence</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>p = Prosite.compile(<span class="py-string">"[AP](2,3)-D."</span>)
<span class="py-prompt">>>> </span>m = p.search(Seq.Seq(<span class="py-string">"PAD"</span>))
<span class="py-prompt">>>> </span>mapping = m.mapping()
<span class="py-prompt">>>> </span>mapped = m.mapped_pattern()
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> str(m[1]), str(p[mapping[1]]), str(mapped[1])
<span class="py-output">P [AP](2,3) [AP]</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> str(mapped)
<span class="py-output">[AP]-[AP]-D.</span>
<span class="py-output"></span><span class="py-prompt">>>></span></pre>
<p>Note that the original term includes the count, while the mapped
pattern does the expansion.</p>
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