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BjornFJohansson · Oct 8, 2024 · 772c429 · 772c429
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b11a49c99066da48d26675bff2f5edc9
+config: ac8ae6f5178219d3fadeb9e68b57bc56
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>Overview: module code &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../_static/jquery.js?v=5d32c60e"></script>
       <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../_static/documentation_options.js?v=56418661"></script>
       <script src="../_static/doctools.js?v=9a2dae69"></script>
       <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>

diff --git a/_modules/pydna.html b/_modules/pydna.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../_static/jquery.js?v=5d32c60e"></script>
       <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../_static/documentation_options.js?v=56418661"></script>
       <script src="../_static/doctools.js?v=9a2dae69"></script>
       <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -218,7 +218,7 @@ <h1>Source code for pydna</h1><div class="highlight"><pre>
 <span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">&quot;Björn Johansson&quot;</span>
 <span class="n">__email__</span> <span class="o">=</span> <span class="s2">&quot;bjorn_johansson@bio.uminho.pt&quot;</span>
 <span class="n">__status__</span> <span class="o">=</span> <span class="s2">&quot;Development&quot;</span>  <span class="c1"># &quot;Production&quot; #&quot;Prototype&quot;</span>
-<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.0.0-post.1+91b3dd0&quot;</span>
+<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.0.0-post.1+30792a3&quot;</span>
 
 
 <span class="c1"># create config directory</span>

diff --git a/_modules/pydna/amplicon.html b/_modules/pydna/amplicon.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.amplicon &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.amplicon &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>

diff --git a/_modules/pydna/amplify.html b/_modules/pydna/amplify.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.amplify &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.amplify &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>

diff --git a/_modules/pydna/assembly.html b/_modules/pydna/assembly.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.assembly &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.assembly &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>

diff --git a/_modules/pydna/common_sub_strings.html b/_modules/pydna/common_sub_strings.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.common_sub_strings &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.common_sub_strings &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>

diff --git a/_modules/pydna/contig.html b/_modules/pydna/contig.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.contig &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.contig &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>

diff --git a/_modules/pydna/design.html b/_modules/pydna/design.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.design &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.design &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
@@ -310,7 +310,7 @@ <h1>Source code for pydna.design</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="assembly_fragments">
 <a class="viewcode-back" href="../../index.html#pydna.design.assembly_fragments">[docs]</a>
-<span class="k">def</span> <span class="nf">assembly_fragments</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">overlap</span><span class="o">=</span><span class="mi">35</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="mi">40</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">assembly_fragments</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">overlap</span><span class="o">=</span><span class="mi">35</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span> <span class="n">circular</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;This function return a list of :mod:`pydna.amplicon.Amplicon` objects where</span>
 <span class="sd">    primers have been modified with tails so that the fragments can be fused in</span>
 <span class="sd">    the order they appear in the list by for example Gibson assembly or homologous</span>
@@ -637,6 +637,9 @@ <h1>Source code for pydna.design</h1><div class="highlight"><pre>
 <span class="sd">    maxlink : int, optional</span>
 <span class="sd">        Maximum length of spacer sequences that may be present in f. These will be included in tails for designed primers.</span>
 
+<span class="sd">    circular : bool, optional</span>
+<span class="sd">        If True, the assembly is circular. If False, the assembly is linear.</span>
+
 <span class="sd">    Returns</span>
 <span class="sd">    -------</span>
 <span class="sd">    seqs : list of :mod:`pydna.amplicon.Amplicon` and other Dseqrecord like objects :mod:`pydna.amplicon.Amplicon` objects</span>
@@ -694,6 +697,15 @@ <h1>Source code for pydna.design</h1><div class="highlight"><pre>
 <span class="sd">    &gt;&gt;&gt;</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="c1"># Recursive call for circular assemblies</span>
+    <span class="k">if</span> <span class="n">circular</span><span class="p">:</span>
+        <span class="n">fragments</span> <span class="o">=</span> <span class="n">assembly_fragments</span><span class="p">(</span><span class="n">f</span> <span class="o">+</span> <span class="n">f</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="n">overlap</span><span class="o">=</span><span class="n">overlap</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="n">maxlink</span><span class="p">,</span> <span class="n">circular</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s2">&quot;template&quot;</span><span class="p">):</span>
+            <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">_pcr</span><span class="p">((</span><span class="n">fragments</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">forward_primer</span><span class="p">,</span> <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reverse_primer</span><span class="p">),</span> <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">template</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">fragments</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
     <span class="c1"># sanity check for arguments</span>
     <span class="n">nf</span> <span class="o">=</span> <span class="p">[</span><span class="n">item</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">f</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">item</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">maxlink</span><span class="p">]</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s2">&quot;template&quot;</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s2">&quot;template&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">nf</span><span class="p">,</span> <span class="n">nf</span><span class="p">[</span><span class="mi">1</span><span class="p">:])):</span>
@@ -819,11 +831,19 @@ <h1>Source code for pydna.design</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="circular_assembly_fragments">
 <a class="viewcode-back" href="../../index.html#pydna.design.circular_assembly_fragments">[docs]</a>
 <span class="k">def</span> <span class="nf">circular_assembly_fragments</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">overlap</span><span class="o">=</span><span class="mi">35</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="mi">40</span><span class="p">):</span>
-    <span class="n">fragments</span> <span class="o">=</span> <span class="n">assembly_fragments</span><span class="p">(</span><span class="n">f</span> <span class="o">+</span> <span class="n">f</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="n">overlap</span><span class="o">=</span><span class="n">overlap</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="n">maxlink</span><span class="p">)</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Equivalent to `assembly_fragments` with `circular=True`.</span>
 
-    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s2">&quot;template&quot;</span><span class="p">):</span>
-        <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">_pcr</span><span class="p">((</span><span class="n">fragments</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">forward_primer</span><span class="p">,</span> <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reverse_primer</span><span class="p">),</span> <span class="n">fragments</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">template</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">fragments</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></div>
+<span class="sd">    Deprecated, kept for backward compatibility. Use `assembly_fragments` with `circular=True` instead.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="kn">import</span> <span class="nn">warnings</span>
+
+    <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
+        <span class="s2">&quot;The circular_assembly_fragments function is deprecated. Use assembly_fragments with circular=True instead.&quot;</span><span class="p">,</span>
+        <span class="ne">DeprecationWarning</span><span class="p">,</span>
+        <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="k">return</span> <span class="n">assembly_fragments</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">overlap</span><span class="o">=</span><span class="n">overlap</span><span class="p">,</span> <span class="n">maxlink</span><span class="o">=</span><span class="n">maxlink</span><span class="p">,</span> <span class="n">circular</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
 
 
 

diff --git a/_modules/pydna/dseq.html b/_modules/pydna/dseq.html
@@ -5,14 +5,14 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.dseq &mdash; pydna 0.0.0.post1+91b3dd0 documentation</title>
+  <title>pydna.dseq &mdash; pydna 0.0.0.post1+30792a3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=7ab3649f" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=d5e8d14d"></script>
+      <script src="../../_static/documentation_options.js?v=56418661"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>