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<span class="target" id="module-pebl.util"></span><p>Miscellaneous utility functions.</p>
<dl class="function">
<dt id="pebl.util.as_list">
<code class="descclassname">pebl.util.</code><code class="descname">as_list</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.as_list" title="Permalink to this definition">¶</a></dt>
<dd><p>Ensures that the result is a list.</p>
<p>If input is a list/tuple/set, return it.
If it’s None, return empty list.
Else, return a list with input as the only element.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.autoassign">
<code class="descclassname">pebl.util.</code><code class="descname">autoassign</code><span class="sig-paren">(</span><em>self</em>, <em>locals</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.autoassign" title="Permalink to this definition">¶</a></dt>
<dd><p>Automatically assigns local variables to <cite>self</cite>.
Generally used in <cite>__init__</cite> methods, as in:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">foo</span><span class="p">,</span> <span class="n">bar</span><span class="p">,</span> <span class="n">baz</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="n">autoassign</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">locals</span><span class="p">())</span>
</pre></div>
</div>
</dd></dl>
<dl class="function">
<dt id="pebl.util.cartesian_product">
<code class="descclassname">pebl.util.</code><code class="descname">cartesian_product</code><span class="sig-paren">(</span><em>list_of_lists</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.cartesian_product" title="Permalink to this definition">¶</a></dt>
<dd><p>Given n lists (or sets), generate all n-tuple combinations.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">list</span><span class="p">(</span><span class="n">cartesian_product</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="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="s2">"foo"</span><span class="p">]]))</span>
<span class="go">[(0, 0), (0, 1), (0, 'foo'), (1, 0), (1, 1), (1, 'foo')]</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">list</span><span class="p">(</span><span class="n">cartesian_product</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="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],</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="go">[(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1), (1, 0, 0), (1, 0, 1), (1, 1, 0), (1, 1, 1)]</span>
</pre></div>
</div>
</dd></dl>
<dl class="function">
<dt id="pebl.util.cond">
<code class="descclassname">pebl.util.</code><code class="descname">cond</code><span class="sig-paren">(</span><em>condition</em>, <em>expr1</em>, <em>expr2</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.cond" title="Permalink to this definition">¶</a></dt>
<dd><p>Marked for deletion.. Python2.5 provides this.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.edit_distance">
<code class="descclassname">pebl.util.</code><code class="descname">edit_distance</code><span class="sig-paren">(</span><em>network1</em>, <em>network2</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.edit_distance" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the edit distance between two networks.</p>
<p>This is a good (but not the only one) metric for determining similarity
between two networks.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.entropy_of_list">
<code class="descclassname">pebl.util.</code><code class="descname">entropy_of_list</code><span class="sig-paren">(</span><em>lst</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.entropy_of_list" title="Permalink to this definition">¶</a></dt>
<dd><p>Given a list of values, generate histogram and calculate the entropy.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.extended_property">
<code class="descclassname">pebl.util.</code><code class="descname">extended_property</code><span class="sig-paren">(</span><em>func</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.extended_property" title="Permalink to this definition">¶</a></dt>
<dd><p>Function decorator for defining property attributes</p>
<p>The decorated function is expected to return a dictionary
containing one or more of the following pairs:</p>
<blockquote>
<div><ul class="simple">
<li>fget - function for getting attribute value</li>
<li>fset - function for setting attribute value</li>
<li>fdel - function for deleting attribute</li>
</ul>
</div></blockquote>
</dd></dl>
<dl class="function">
<dt id="pebl.util.flatten">
<code class="descclassname">pebl.util.</code><code class="descname">flatten</code><span class="sig-paren">(</span><em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.flatten" title="Permalink to this definition">¶</a></dt>
<dd><p>Given a nested datastructure, flatten it.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.levenshtein">
<code class="descclassname">pebl.util.</code><code class="descname">levenshtein</code><span class="sig-paren">(</span><em>a</em>, <em>b</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.levenshtein" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates the Levenshtein distance between <em>strings</em> a and b.</p>
<p>from <a class="reference external" href="http://hetland.org/coding/python/levenshtein.py">http://hetland.org/coding/python/levenshtein.py</a></p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.logadd">
<code class="descclassname">pebl.util.</code><code class="descname">logadd</code><span class="sig-paren">(</span><em>x</em>, <em>y</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.logadd" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds two log values.</p>
<p>Ensures accuracy even when the difference between values is large.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.logscale_probwheel">
<code class="descclassname">pebl.util.</code><code class="descname">logscale_probwheel</code><span class="sig-paren">(</span><em>items</em>, <em>logweights</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.logscale_probwheel" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly select an item from a [log] weighted list of items.</p>
<p>Fucntion just rescale logweights and exponentiates before calling
probwheel.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.logsum">
<code class="descclassname">pebl.util.</code><code class="descname">logsum</code><span class="sig-paren">(</span><em>lst</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.logsum" title="Permalink to this definition">¶</a></dt>
<dd><p>Sums a list of log values, ensuring accuracy.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.lru_cache">
<code class="descclassname">pebl.util.</code><code class="descname">lru_cache</code><span class="sig-paren">(</span><em>maxsize</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.lru_cache" title="Permalink to this definition">¶</a></dt>
<dd><p>Decorator applying a least-recently-used cache with the given maximum size.</p>
<p>Arguments to the cached function must be hashable.
Cache performance statistics stored in f.hits and f.misses.</p>
<p>from <a class="reference external" href="http://code.activestate.com/recipes/498245/">http://code.activestate.com/recipes/498245/</a></p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.nestediter">
<code class="descclassname">pebl.util.</code><code class="descname">nestediter</code><span class="sig-paren">(</span><em>lst1</em>, <em>lst2</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.nestediter" title="Permalink to this definition">¶</a></dt>
<dd><p>A syntactic shortform for doing nested loops.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.normalize">
<code class="descclassname">pebl.util.</code><code class="descname">normalize</code><span class="sig-paren">(</span><em>lst</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.normalize" title="Permalink to this definition">¶</a></dt>
<dd><p>Normalizes a list of numbers (sets sum to 1.0).</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.probwheel">
<code class="descclassname">pebl.util.</code><code class="descname">probwheel</code><span class="sig-paren">(</span><em>items</em>, <em>weights</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.probwheel" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly select an item from a weighted list of items.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.rescale_logvalues">
<code class="descclassname">pebl.util.</code><code class="descname">rescale_logvalues</code><span class="sig-paren">(</span><em>lst</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.rescale_logvalues" title="Permalink to this definition">¶</a></dt>
<dd><p>Rescales a list of log values by setting max value to 0.0</p>
<p>This function is necessary when working with list of log values. Without
it, we could have overflows. This is a lot faster than using arbitrary
precision math libraries.</p>
</dd></dl>
<dl class="function">
<dt id="pebl.util.unzip">
<code class="descclassname">pebl.util.</code><code class="descname">unzip</code><span class="sig-paren">(</span><em>l</em>, <em>*jj</em><span class="sig-paren">)</span><a class="headerlink" href="#pebl.util.unzip" title="Permalink to this definition">¶</a></dt>
<dd><p>Opposite of zip().</p>
<p>jj is a tuple of list indexes (or keys) to extract or unzip. If not
specified, all items are unzipped.</p>
</dd></dl>
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