Update from scikit-bio/scikit-bio@34d7bbf

scikit-bio · Jan 10, 2025 · b3f0438 · b3f0438
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diff --git a/docs/dev/_static/pygments.css b/docs/dev/_static/pygments.css
diff --git a/docs/dev/alignment.html b/docs/dev/alignment.html
@@ -31,7 +31,7 @@
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 <link href="_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=8f2a1f02" />
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@@ -754,7 +754,7 @@ <h2>Tutorial<a class="headerlink" href="#tutorial" title="Link to this heading">
 <h3>Alignment data structure<a class="headerlink" href="#alignment-data-structure" title="Link to this heading">#</a></h3>
 <p>Load two DNA sequences that have been previously aligned into a <code class="docutils literal notranslate"><span class="pre">TabularMSA</span></code>
 object, using sequence IDs as the MSA’s index:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">TabularMSA</span><span class="p">,</span> <span class="n">DNA</span>
+<div class="doctest highlight-default 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">skbio</span><span class="w"> </span><span class="kn">import</span> <span class="n">TabularMSA</span><span class="p">,</span> <span class="n">DNA</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">seqs</span> <span class="o">=</span> <span class="p">[</span><span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;ACC--G-GGTA..&quot;</span><span class="p">,</span> <span class="n">metadata</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s2">&quot;seq1&quot;</span><span class="p">}),</span>
 <span class="gp">... </span>        <span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;TCC--G-GGCA..&quot;</span><span class="p">,</span> <span class="n">metadata</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s2">&quot;seq2&quot;</span><span class="p">})]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">msa</span> <span class="o">=</span> <span class="n">TabularMSA</span><span class="p">(</span><span class="n">seqs</span><span class="p">,</span> <span class="n">minter</span><span class="o">=</span><span class="s1">&#39;id&#39;</span><span class="p">)</span>
@@ -775,7 +775,7 @@ <h3>Alignment data structure<a class="headerlink" href="#alignment-data-structur
 <section id="using-the-optimized-alignment-algorithm">
 <h3>Using the optimized alignment algorithm<a class="headerlink" href="#using-the-optimized-alignment-algorithm" title="Link to this heading">#</a></h3>
 <p>Using the convenient <code class="docutils literal notranslate"><span class="pre">local_pairwise_align_ssw</span></code> function:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio.alignment</span> <span class="kn">import</span> <span class="n">local_pairwise_align_ssw</span>
+<div class="doctest highlight-default 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">skbio.alignment</span><span class="w"> </span><span class="kn">import</span> <span class="n">local_pairwise_align_ssw</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignment</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">start_end_positions</span> <span class="o">=</span> <span class="n">local_pairwise_align_ssw</span><span class="p">(</span>
 <span class="gp">... </span>    <span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;ACTAAGGCTCTCTACCCCTCTCAGAGA&quot;</span><span class="p">),</span>
 <span class="gp">... </span>    <span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;ACTAAGGCTCCTAACCCCCTTTTCTCAGA&quot;</span><span class="p">)</span>
@@ -796,7 +796,7 @@ <h3>Using the optimized alignment algorithm<a class="headerlink" href="#using-th
 </pre></div>
 </div>
 <p>Using the <code class="docutils literal notranslate"><span class="pre">StripedSmithWaterman</span></code> object:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio.alignment</span> <span class="kn">import</span> <span class="n">StripedSmithWaterman</span>
+<div class="doctest highlight-default 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">skbio.alignment</span><span class="w"> </span><span class="kn">import</span> <span class="n">StripedSmithWaterman</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">query</span> <span class="o">=</span> <span class="n">StripedSmithWaterman</span><span class="p">(</span><span class="s2">&quot;ACTAAGGCTCTCTACCCCTCTCAGAGA&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignment</span> <span class="o">=</span> <span class="n">query</span><span class="p">(</span><span class="s2">&quot;AAAAAACTCTCTAAACTCACTAAGGCTCTCTACCCCTCTTCAGAGAAGTCGA&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">alignment</span><span class="p">)</span>
@@ -808,7 +808,7 @@ <h3>Using the optimized alignment algorithm<a class="headerlink" href="#using-th
 </div>
 <p>Using the <code class="docutils literal notranslate"><span class="pre">StripedSmithWaterman</span></code> object for multiple targets in an efficient
 way and finding the aligned sequence representations:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio.alignment</span> <span class="kn">import</span> <span class="n">StripedSmithWaterman</span>
+<div class="doctest highlight-default 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">skbio.alignment</span><span class="w"> </span><span class="kn">import</span> <span class="n">StripedSmithWaterman</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignments</span> <span class="o">=</span> <span class="p">[]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">target_sequences</span> <span class="o">=</span> <span class="p">[</span>
 <span class="gp">... </span>    <span class="s2">&quot;GCTAACTAGGCTCCCTTCTACCCCTCTCAGAGA&quot;</span><span class="p">,</span>
@@ -848,8 +848,8 @@ <h3>Using the slow alignment algorithm<a class="headerlink" href="#using-the-slo
 <p>Here we locally align a pair of protein sequences using gap open penalty
 of 11 and a gap extend penalty of 1 (in other words, it is much more
 costly to open a new gap than extend an existing one).</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">Protein</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio.alignment</span> <span class="kn">import</span> <span class="n">local_pairwise_align_protein</span>
+<div class="doctest highlight-default 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">skbio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Protein</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.alignment</span><span class="w"> </span><span class="kn">import</span> <span class="n">local_pairwise_align_protein</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">s1</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s2">&quot;HEAGAWGHEE&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">s2</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s2">&quot;PAWHEAE&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignment</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">start_end_positions</span> <span class="o">=</span> <span class="n">local_pairwise_align_protein</span><span class="p">(</span>
@@ -874,8 +874,8 @@ <h3>Using the slow alignment algorithm<a class="headerlink" href="#using-the-slo
 </pre></div>
 </div>
 <p>Similarly, we can perform global alignment of nucleotide sequences:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">DNA</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio.alignment</span> <span class="kn">import</span> <span class="n">global_pairwise_align_nucleotide</span>
+<div class="doctest highlight-default 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">skbio</span><span class="w"> </span><span class="kn">import</span> <span class="n">DNA</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.alignment</span><span class="w"> </span><span class="kn">import</span> <span class="n">global_pairwise_align_nucleotide</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">s1</span> <span class="o">=</span> <span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;GCGTGCCTAAGGTATGCAAG&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">s2</span> <span class="o">=</span> <span class="n">DNA</span><span class="p">(</span><span class="s2">&quot;ACGTGCCTAGGTACGCAAG&quot;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">alignment</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">start_end_positions</span> <span class="o">=</span> <span class="n">global_pairwise_align_nucleotide</span><span class="p">(</span>
@@ -981,7 +981,7 @@ <h3>Using the slow alignment algorithm<a class="headerlink" href="#using-the-slo
 
   <p class="copyright">
 
-      © Copyright 2014-2024, scikit-bio development team.
+      © Copyright 2014-2025, scikit-bio development team.
       <br/>
 
   </p>