Merge pull request #54 from matsengrp/mlepatch

Mlepatch

Author: wsdewitt

Diff for: docs/_images/gctree.out.inference.abundance_rank.svg

@@ -511,7 +511,7 @@ <h1>Source code for gctree.branching_processes</h1><div class="highlight"><pre>
 <span class="sd">        Returns:</span>
 <span class="sd">            Tuple :math:`(p, q)` with estimated branching probability and estimated mutation probability</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">_mle_helper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ll</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">_mle_helper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ll</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="CollapsedTree.simulate"><a class="viewcode-back" href="../../stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.simulate">[docs]</a>    <span class="k">def</span> <span class="nf">simulate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">,</span> <span class="n">q</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">,</span> <span class="n">root</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
         <span class="sa">r</span><span class="sd">&quot;&quot;&quot;Simulate a collapsed tree as an infinite type Galton-Watson process</span>
@@ -627,7 +627,9 @@ <h1>Source code for gctree.branching_processes</h1><div class="highlight"><pre>
             <span class="n">nstyle</span> <span class="o">=</span> <span class="n">ete3</span><span class="o">.</span><span class="n">NodeStyle</span><span class="p">()</span>
             <span class="n">nstyle</span><span class="p">[</span><span class="s2">&quot;size&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
             <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">up</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">sequence</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span> <span class="o">==</span> <span class="nb">set</span><span class="p">(</span><span class="s2">&quot;ACGT&quot;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="s2">&quot;sequence&quot;</span> <span class="ow">in</span> <span class="n">tree_copy</span><span class="o">.</span><span class="n">features</span> <span class="ow">and</span> <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">node</span><span class="o">.</span><span class="n">sequence</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+                <span class="p">)</span> <span class="o">==</span> <span class="nb">set</span><span class="p">(</span><span class="s2">&quot;ACGT&quot;</span><span class="p">):</span>
                     <span class="k">if</span> <span class="n">frame</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
                         <span class="k">if</span> <span class="n">chain_split</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">frame2</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
@@ -699,7 +701,6 @@ <h1>Source code for gctree.branching_processes</h1><div class="highlight"><pre>
         <span class="n">ts</span><span class="o">.</span><span class="n">layout_fn</span> <span class="o">=</span> <span class="n">my_layout</span>
         <span class="n">ts</span><span class="o">.</span><span class="n">show_scale</span> <span class="o">=</span> <span class="kc">False</span>
         <span class="n">ts</span><span class="o">.</span><span class="n">show_branch_support</span> <span class="o">=</span> <span class="n">show_support</span>
-        <span class="n">tree_copy</span><span class="o">.</span><span class="n">render</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">tree_style</span><span class="o">=</span><span class="n">ts</span><span class="p">)</span>
         <span class="c1"># if we labelled seqs, let&#39;s also write the alignment out so we have</span>
         <span class="c1"># the sequences (including of internal nodes)</span>
         <span class="k">if</span> <span class="n">idlabel</span><span class="p">:</span>
@@ -714,7 +715,8 @@ <h1>Source code for gctree.branching_processes</h1><div class="highlight"><pre>
                 <span class="p">)</span>
             <span class="n">AlignIO</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
                 <span class="n">aln</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">outfile</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot;.fasta&quot;</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">),</span> <span class="s2">&quot;fasta&quot;</span>
-            <span class="p">)</span></div>
+            <span class="p">)</span>
+        <span class="k">return</span> <span class="n">tree_copy</span><span class="o">.</span><span class="n">render</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">tree_style</span><span class="o">=</span><span class="n">ts</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="CollapsedTree.write"><a class="viewcode-back" href="../../stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
         <span class="sa">r</span><span class="sd">&quot;&quot;&quot;Serialize to pickle file.</span>
@@ -1003,7 +1005,7 @@ <h1>Source code for gctree.branching_processes</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">ls</span><span class="o">.</span><span class="n">sum</span><span class="p">(),</span> <span class="n">grad_ls</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="CollapsedForest.mle"><a class="viewcode-back" href="../../stubs/gctree.CollapsedForest.html#gctree.CollapsedForest.mle">[docs]</a>    <span class="k">def</span> <span class="nf">mle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">]:</span>
-        <span class="k">return</span> <span class="n">_mle_helper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ll</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">_mle_helper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ll</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
 
     <span class="n">mle</span><span class="o">.</span><span class="vm">__doc__</span> <span class="o">=</span> <span class="n">CollapsedTree</span><span class="o">.</span><span class="n">mle</span><span class="o">.</span><span class="vm">__doc__</span>
 

Diff for: docs/_images/gctree.out.inference.likelihood_rank.svg

@@ -472,7 +472,7 @@ <h1>Source code for gctree.mutation_model</h1><div class="highlight"><pre>
                         <span class="n">child</span><span class="o">.</span><span class="n">add_feature</span><span class="p">(</span><span class="s2">&quot;time&quot;</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
                         <span class="n">leaf</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">child</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="n">leaves_unterminated</span> <span class="o">&lt;</span> <span class="n">N</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">N</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">leaves_unterminated</span> <span class="o">&lt;</span> <span class="n">N</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span>
                 <span class="s2">&quot;tree terminated with </span><span class="si">{}</span><span class="s2"> leaves, </span><span class="si">{}</span><span class="s2"> desired&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
                     <span class="n">leaves_unterminated</span><span class="p">,</span> <span class="n">N</span>

Diff for: docs/_modules/gctree/branching_processes.html

@@ -22,7 +22,7 @@ Lint::
 
   make lint
 
-Build docs locally (you can then see the generated documentation in ``docs/_build/index.html``.)::
+Build docs locally (you can then see the generated documentation in ``docsrc/_build/html/index.html``.)::
 
   make docs
 

Diff for: docs/_modules/gctree/mutation_model.html

@@ -197,7 +197,7 @@ <h1>Developer tools<a class="headerlink" href="#developer-tools" title="Permalin
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">lint</span>
 </pre></div>
 </div>
-<p>Build docs locally (you can then see the generated documentation in <code class="docutils literal notranslate"><span class="pre">docs/_build/index.html</span></code>.):</p>
+<p>Build docs locally (you can then see the generated documentation in <code class="docutils literal notranslate"><span class="pre">docsrc/_build/html/index.html</span></code>.):</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">docs</span>
 </pre></div>
 </div>

Diff for: docs/_sources/developer.rst.txt

@@ -22,7 +22,7 @@ Lint::
 
   make lint
 
-Build docs locally (you can then see the generated documentation in ``docs/_build/index.html``.)::
+Build docs locally (you can then see the generated documentation in ``docsrc/_build/html/index.html``.)::
 
   make docs
 

Diff for: docs/developer.html

@@ -334,7 +334,7 @@ def mle(self, **kwargs) -> Tuple[np.float64, np.float64]:
         Returns:
             Tuple :math:`(p, q)` with estimated branching probability and estimated mutation probability
         """
-        return _mle_helper(self.ll)
+        return _mle_helper(self.ll, **kwargs)
 
     def simulate(self, p: np.float64, q: np.float64, root: bool = True):
         r"""Simulate a collapsed tree as an infinite type Galton-Watson process
@@ -450,7 +450,9 @@ def my_layout(node):
             nstyle = ete3.NodeStyle()
             nstyle["size"] = 0
             if node.up is not None:
-                if set(node.sequence.upper()) == set("ACGT"):
+                if "sequence" in tree_copy.features and set(
+                    node.sequence.upper()
+                ) == set("ACGT"):
                     if frame is not None:
                         if chain_split is not None and frame2 is None:
                             raise ValueError(
@@ -522,7 +524,6 @@ def my_layout(node):
         ts.layout_fn = my_layout
         ts.show_scale = False
         ts.show_branch_support = show_support
-        tree_copy.render(outfile, tree_style=ts)
         # if we labelled seqs, let's also write the alignment out so we have
         # the sequences (including of internal nodes)
         if idlabel:
@@ -538,6 +539,7 @@ def my_layout(node):
             AlignIO.write(
                 aln, open(os.path.splitext(outfile)[0] + ".fasta", "w"), "fasta"
             )
+        return tree_copy.render(outfile, tree_style=ts)
 
     def write(self, file_name: str):
         r"""Serialize to pickle file.
@@ -826,7 +828,7 @@ def ll(
             return ls.sum(), grad_ls.sum(axis=0)
 
     def mle(self, **kwargs) -> Tuple[np.float64, np.float64]:
-        return _mle_helper(self.ll)
+        return _mle_helper(self.ll, **kwargs)
 
     mle.__doc__ = CollapsedTree.mle.__doc__
 

Diff for: docsrc/developer.rst

@@ -295,7 +295,7 @@ def simulate(
                         child.add_feature("time", t)
                         leaf.add_child(child)
 
-        if leaves_unterminated < N:
+        if N is not None and leaves_unterminated < N:
             raise RuntimeError(
                 "tree terminated with {} leaves, {} desired".format(
                     leaves_unterminated, N