Automated update 66ad0a062e98f9964a7a4c67ad85291386ef3540

Author: Sphinx

dev/Tutorial/chapter_align.html

@@ -73,8 +73,8 @@
 </li>
 <li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#generalized-pairwise-alignments">Generalized pairwise alignments</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-a-substitution-matrix-and-alphabet">Generalized pairwise alignments using a substitution matrix and alphabet</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-match-mismatch-scores-and-an-alphabet">Generalized pairwise alignments using match/mismatch scores and an alphabet</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-a-substitution-matrix">Generalized pairwise alignments using a substitution matrix</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-match-mismatch-scores">Generalized pairwise alignments using match/mismatch scores</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-match-mismatch-scores-and-integer-sequences">Generalized pairwise alignments using match/mismatch scores and integer sequences</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#generalized-pairwise-alignments-using-a-substitution-matrix-and-integer-sequences">Generalized pairwise alignments using a substitution matrix and integer sequences</a></li>
 </ul>
@@ -1176,9 +1176,7 @@ <h3>Array objects<a class="headerlink" href="#array-objects" title="Link to this
 <span class="go">&#39;ACGT&#39;</span>
 </pre></div>
 </div>
-<p>This property is read-only; modifying the underlying <code class="docutils literal notranslate"><span class="pre">_alphabet</span></code>
-attribute may lead to unexpected results. Elements can be accessed both
-by letter and by integer index:</p>
+<p>Elements can be accessed both by letter and by integer index:</p>
 <div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">counts</span><span class="p">[</span><span class="s2">&quot;C&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="mi">3</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">counts</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">7</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">counts</span><span class="p">)</span>
@@ -1810,8 +1808,8 @@ <h3>Loading predefined substitution matrices<a class="headerlink" href="#loading
 nucleotides or amino acids. More generally, <code class="docutils literal notranslate"><span class="pre">PairwiseAligner</span></code> can also
 be applied to lists or tuples of arbitrary objects. This section will
 describe some examples of such generalized pairwise alignments.</p>
-<section id="generalized-pairwise-alignments-using-a-substitution-matrix-and-alphabet">
-<h3>Generalized pairwise alignments using a substitution matrix and alphabet<a class="headerlink" href="#generalized-pairwise-alignments-using-a-substitution-matrix-and-alphabet" title="Link to this heading"></a></h3>
+<section id="generalized-pairwise-alignments-using-a-substitution-matrix">
+<h3>Generalized pairwise alignments using a substitution matrix<a class="headerlink" href="#generalized-pairwise-alignments-using-a-substitution-matrix" title="Link to this heading"></a></h3>
 <p>Schneider <em>et al.</em> <a class="reference internal" href="chapter_bibliography.html#schneider2005" id="id11"><span>[Schneider2005]</span></a> created a
 substitution matrix for aligning three-nucleotide codons (see
 <a class="reference external" href="#codonmatrix">below</a> in section <a class="reference internal" href="#sec-substitution-matrices"><span class="std std-ref">Substitution matrices</span></a>
@@ -1877,28 +1875,19 @@ <h3>Generalized pairwise alignments using a substitution matrix and alphabet<a c
 </pre></div>
 </div>
 </section>
-<section id="generalized-pairwise-alignments-using-match-mismatch-scores-and-an-alphabet">
-<h3>Generalized pairwise alignments using match/mismatch scores and an alphabet<a class="headerlink" href="#generalized-pairwise-alignments-using-match-mismatch-scores-and-an-alphabet" title="Link to this heading"></a></h3>
+<section id="generalized-pairwise-alignments-using-match-mismatch-scores">
+<h3>Generalized pairwise alignments using match/mismatch scores<a class="headerlink" href="#generalized-pairwise-alignments-using-match-mismatch-scores" title="Link to this heading"></a></h3>
 <p>Using the three-letter amino acid symbols, the sequences above translate
 to</p>
 <div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">s1</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;Asn&quot;</span><span class="p">,</span> <span class="s2">&quot;Leu&quot;</span><span class="p">,</span> <span class="s2">&quot;Leu&quot;</span><span class="p">,</span> <span class="s2">&quot;Phe&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">s2</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;Asn&quot;</span><span class="p">,</span> <span class="s2">&quot;Leu&quot;</span><span class="p">,</span> <span class="s2">&quot;Phe&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>We can align these sequences directly to each other by using a
-three-letter amino acid alphabet:</p>
-<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Align</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span> <span class="o">=</span> <span class="n">Align</span><span class="o">.</span><span class="n">PairwiseAligner</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span><span class="o">.</span><span class="n">alphabet</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Ala&#39;</span><span class="p">,</span> <span class="s1">&#39;Arg&#39;</span><span class="p">,</span> <span class="s1">&#39;Asn&#39;</span><span class="p">,</span> <span class="s1">&#39;Asp&#39;</span><span class="p">,</span> <span class="s1">&#39;Cys&#39;</span><span class="p">,</span>
-<span class="gp">... </span>                    <span class="s1">&#39;Gln&#39;</span><span class="p">,</span> <span class="s1">&#39;Glu&#39;</span><span class="p">,</span> <span class="s1">&#39;Gly&#39;</span><span class="p">,</span> <span class="s1">&#39;His&#39;</span><span class="p">,</span> <span class="s1">&#39;Ile&#39;</span><span class="p">,</span>
-<span class="gp">... </span>                    <span class="s1">&#39;Leu&#39;</span><span class="p">,</span> <span class="s1">&#39;Lys&#39;</span><span class="p">,</span> <span class="s1">&#39;Met&#39;</span><span class="p">,</span> <span class="s1">&#39;Phe&#39;</span><span class="p">,</span> <span class="s1">&#39;Pro&#39;</span><span class="p">,</span>
-<span class="gp">... </span>                    <span class="s1">&#39;Ser&#39;</span><span class="p">,</span> <span class="s1">&#39;Thr&#39;</span><span class="p">,</span> <span class="s1">&#39;Trp&#39;</span><span class="p">,</span> <span class="s1">&#39;Tyr&#39;</span><span class="p">,</span> <span class="s1">&#39;Val&#39;</span><span class="p">]</span>  <span class="c1"># fmt: skip</span>
-<span class="gp">...</span>
-</pre></div>
-</div>
 <p>We use +6/-1 match and mismatch scores as an approximation of the
 BLOSUM62 matrix, and align these sequences to each other:</p>
-<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span><span class="o">.</span><span class="n">match</span> <span class="o">=</span> <span class="o">+</span><span class="mi">6</span>
+<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Align</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span> <span class="o">=</span> <span class="n">Align</span><span class="o">.</span><span class="n">PairwiseAligner</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span><span class="o">.</span><span class="n">match</span> <span class="o">=</span> <span class="o">+</span><span class="mi">6</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span><span class="o">.</span><span class="n">mismatch</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignments</span> <span class="o">=</span> <span class="n">aligner</span><span class="o">.</span><span class="n">align</span><span class="p">(</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">alignments</span><span class="p">))</span>
@@ -1920,9 +1909,10 @@ <h3>Generalized pairwise alignments using match/mismatch scores and an alphabet<
 </section>
 <section id="generalized-pairwise-alignments-using-match-mismatch-scores-and-integer-sequences">
 <h3>Generalized pairwise alignments using match/mismatch scores and integer sequences<a class="headerlink" href="#generalized-pairwise-alignments-using-match-mismatch-scores-and-integer-sequences" title="Link to this heading"></a></h3>
-<p>Internally, the first step when performing an alignment is to replace
-the two sequences by integer arrays consisting of the indices of each
-letter in each sequence in the alphabet associated with the aligner.
+<p>Internally, the first step when performing an alignment is to create a
+temporary alphabet consisting of the letters in the two sequences, and
+replacing the sequences by integer arrays consisting of the indices of each
+letter in the alphabet.
 This step can be bypassed by passing integer arrays directly:</p>
 <div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Align</span>
@@ -1986,11 +1976,11 @@ <h3>Generalized pairwise alignments using a substitution matrix and integer sequ
 <span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span> <span class="o">=</span> <span class="n">Align</span><span class="o">.</span><span class="n">PairwiseAligner</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">m</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">:]</span> <span class="o">=</span> <span class="n">m</span><span class="p">[</span><span class="mi">1</span><span class="p">:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="mi">2</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">m</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">3</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">m</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">6</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
 <span class="go">[[ 1. -2. -2. -2. -2.]</span>
 <span class="go"> [-2.  1.  0.  0.  0.]</span>
-<span class="go"> [-2.  0.  3.  0.  0.]</span>
+<span class="go"> [-2.  0.  6.  0.  0.]</span>
 <span class="go"> [-2.  0.  0.  1.  0.]</span>
 <span class="go"> [-2.  0.  0.  0.  1.]]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">aligner</span><span class="o">.</span><span class="n">substitution_matrix</span> <span class="o">=</span> <span class="n">m</span>
@@ -2011,7 +2001,7 @@ <h3>Generalized pairwise alignments using a substitution matrix and integer sequ
 <span class="go">0 3 2 - 1</span>
 
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">alignments</span><span class="o">.</span><span class="n">score</span><span class="p">)</span>
-<span class="go">2.0</span>
+<span class="go">5.0</span>
 </pre></div>
 </div>
 </section>