Add subpackage docstrings

kkrismer · Jun 15, 2021 · 0b97db6 · 0b97db6
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diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/seqgra.comparator.html b/docs/seqgra.comparator.html
@@ -212,6 +212,18 @@
 
   <div class="section" id="module-seqgra.comparator">
 <span id="seqgra-comparator-package"></span><h1>seqgra.comparator package<a class="headerlink" href="#module-seqgra.comparator" title="Permalink to this headline">¶</a></h1>
+<p>seqgra comparators used by <cite>seqgras</cite> command</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="seqgra.comparator.comparator.html#seqgra.comparator.comparator.Comparator" title="seqgra.comparator.comparator.Comparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">Comparator</span></code></a>: abstract base class for all comparators</p></li>
+<li><p><a class="reference internal" href="seqgra.comparator.curvetablecomparator.html#seqgra.comparator.curvetablecomparator.CurveTableComparator" title="seqgra.comparator.curvetablecomparator.CurveTableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">CurveTableComparator</span></code></a>: collects PR and ROC curve information in text file</p></li>
+<li><p><a class="reference internal" href="seqgra.comparator.fietablecomparator.html#seqgra.comparator.fietablecomparator.FIETableComparator" title="seqgra.comparator.fietablecomparator.FIETableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">FIETableComparator</span></code></a>: collects feature importance evaluator information in text file</p></li>
+<li><p><a class="reference internal" href="seqgra.comparator.prcomparator.html#seqgra.comparator.prcomparator.PRComparator" title="seqgra.comparator.prcomparator.PRComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">PRComparator</span></code></a>: creates PR curves from various grammars and architectures</p></li>
+<li><p><a class="reference internal" href="seqgra.comparator.roccomparator.html#seqgra.comparator.roccomparator.ROCComparator" title="seqgra.comparator.roccomparator.ROCComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">ROCComparator</span></code></a>: creates ROC curves from various grammars and architectures</p></li>
+<li><p><a class="reference internal" href="seqgra.comparator.tablecomparator.html#seqgra.comparator.tablecomparator.TableComparator" title="seqgra.comparator.tablecomparator.TableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">TableComparator</span></code></a>: collects grammar and model information in text file</p></li>
+</ul>
+</dd>
+</dl>
 <div class="section" id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">

diff --git a/docs/seqgra.evaluator.gradientbased.html b/docs/seqgra.evaluator.gradientbased.html
@@ -212,6 +212,29 @@
 
   <div class="section" id="module-seqgra.evaluator.gradientbased">
 <span id="seqgra-evaluator-gradientbased-package"></span><h1>seqgra.evaluator.gradientbased package<a class="headerlink" href="#module-seqgra.evaluator.gradientbased" title="Permalink to this headline">¶</a></h1>
+<p>seqgra evaluator hierarchy - gradient-based feature importance evaluators (FIE)</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.gradientbasedevaluator.html#seqgra.evaluator.gradientbased.gradientbasedevaluator.GradientBasedEvaluator" title="seqgra.evaluator.gradientbased.gradientbasedevaluator.GradientBasedEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">GradientBasedEvaluator</span></code></a>: abstract class for all gradient-based feature importance evaluators</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator.html#seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator.AbstractDifferenceGradientEvaluator" title="seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator.AbstractDifferenceGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractDifferenceGradientEvaluator</span></code></a>: abstract class for difference-based gradient-based feature importance evaluators</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.abstractgradientevaluator.html#seqgra.evaluator.gradientbased.abstractgradientevaluator.AbstractGradientEvaluator" title="seqgra.evaluator.gradientbased.abstractgradientevaluator.AbstractGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractGradientEvaluator</span></code></a>: abstract class for baseline-based gradient-based feature importance evaluators</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator.html#seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator.ContrastiveExcitationBackpropEvaluator" title="seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator.ContrastiveExcitationBackpropEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">ContrastiveExcitationBackpropEvaluator</span></code></a>: contrastive excitation backprop FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.deconvevaluator.html#seqgra.evaluator.gradientbased.deconvevaluator.DeconvEvaluator" title="seqgra.evaluator.gradientbased.deconvevaluator.DeconvEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">DeconvEvaluator</span></code></a>: deconvolution FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.deepliftevaluator.html#seqgra.evaluator.gradientbased.deepliftevaluator.DeepLiftEvaluator" title="seqgra.evaluator.gradientbased.deepliftevaluator.DeepLiftEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">DeepLiftEvaluator</span></code></a>: DeepLIFT FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.differencegradientevaluator.html#seqgra.evaluator.gradientbased.differencegradientevaluator.DifferenceGradientEvaluator" title="seqgra.evaluator.gradientbased.differencegradientevaluator.DifferenceGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">DifferenceGradientEvaluator</span></code></a>: difference gradient FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.excitationbackpropevaluator.html#seqgra.evaluator.gradientbased.excitationbackpropevaluator.ExcitationBackpropEvaluator" title="seqgra.evaluator.gradientbased.excitationbackpropevaluator.ExcitationBackpropEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">ExcitationBackpropEvaluator</span></code></a>: excitation backprop FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.feedbackevaluator.html#seqgra.evaluator.gradientbased.feedbackevaluator.FeedbackEvaluator" title="seqgra.evaluator.gradientbased.feedbackevaluator.FeedbackEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">FeedbackEvaluator</span></code></a>: feedback FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.gradcamgradientevaluator.html#seqgra.evaluator.gradientbased.gradcamgradientevaluator.GradCamGradientEvaluator" title="seqgra.evaluator.gradientbased.gradcamgradientevaluator.GradCamGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">GradCamGradientEvaluator</span></code></a>: GradCAM FIE</p></li>
+<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">DifferenceGradientEvaluator</span></code>: difference gradient FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.gradientxinputevaluator.html#seqgra.evaluator.gradientbased.gradientxinputevaluator.GradientxInputEvaluator" title="seqgra.evaluator.gradientbased.gradientxinputevaluator.GradientxInputEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">GradientxInputEvaluator</span></code></a>: gradient times input FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.guidedbackpropevaluator.html#seqgra.evaluator.gradientbased.guidedbackpropevaluator.GuidedBackpropEvaluator" title="seqgra.evaluator.gradientbased.guidedbackpropevaluator.GuidedBackpropEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">GuidedBackpropEvaluator</span></code></a>: guided backprop FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.integratedgradientevaluator.html#seqgra.evaluator.gradientbased.integratedgradientevaluator.IntegratedGradientEvaluator" title="seqgra.evaluator.gradientbased.integratedgradientevaluator.IntegratedGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">IntegratedGradientEvaluator</span></code></a>: Integrated Gradients FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator.html#seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator.NonlinearIntegratedGradientEvaluator" title="seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator.NonlinearIntegratedGradientEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">NonlinearIntegratedGradientEvaluator</span></code></a>: nonlinear Integrated Gradients FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.saliencyevaluator.html#seqgra.evaluator.gradientbased.saliencyevaluator.SaliencyEvaluator" title="seqgra.evaluator.gradientbased.saliencyevaluator.SaliencyEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">SaliencyEvaluator</span></code></a>: absolute gradient (saliency) FIE</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.gradientbased.smoothgradevaluator.html#seqgra.evaluator.gradientbased.smoothgradevaluator.SmoothGradEvaluator" title="seqgra.evaluator.gradientbased.smoothgradevaluator.SmoothGradEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">SmoothGradEvaluator</span></code></a>: smooth grad FIE</p></li>
+</ul>
+</dd>
+</dl>
 <div class="section" id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">

diff --git a/docs/seqgra.evaluator.html b/docs/seqgra.evaluator.html
@@ -218,6 +218,19 @@
 
   <div class="section" id="module-seqgra.evaluator">
 <span id="seqgra-evaluator-package"></span><h1>seqgra.evaluator package<a class="headerlink" href="#module-seqgra.evaluator" title="Permalink to this headline">¶</a></h1>
+<p>seqgra evaluator hierarchy</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="seqgra.evaluator.evaluator.html#seqgra.evaluator.evaluator.Evaluator" title="seqgra.evaluator.evaluator.Evaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">Evaluator</span></code></a>: abstract base class for all evaluators</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.evaluator.html#seqgra.evaluator.evaluator.FeatureImportanceEvaluator" title="seqgra.evaluator.evaluator.FeatureImportanceEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">FeatureImportanceEvaluator</span></code></a>: abstract class for feature importance evaluators</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.metricsevaluator.html#seqgra.evaluator.metricsevaluator.MetricsEvaluator" title="seqgra.evaluator.metricsevaluator.MetricsEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MetricsEvaluator</span></code></a>: metrics evaluator</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.predictevaluator.html#seqgra.evaluator.predictevaluator.PredictEvaluator" title="seqgra.evaluator.predictevaluator.PredictEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">PredictEvaluator</span></code></a>: predict evaluator</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.prevaluator.html#seqgra.evaluator.prevaluator.PREvaluator" title="seqgra.evaluator.prevaluator.PREvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">PREvaluator</span></code></a>: PR curve evaluator</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.rocevaluator.html#seqgra.evaluator.rocevaluator.ROCEvaluator" title="seqgra.evaluator.rocevaluator.ROCEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">ROCEvaluator</span></code></a>: ROC curve evaluator</p></li>
+<li><p><a class="reference internal" href="seqgra.evaluator.sisevaluator.html#seqgra.evaluator.sisevaluator.SISEvaluator" title="seqgra.evaluator.sisevaluator.SISEvaluator"><code class="xref py py-class docutils literal notranslate"><span class="pre">SISEvaluator</span></code></a>: SIS feature importance evaluator</p></li>
+</ul>
+</dd>
+</dl>
 <div class="section" id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">

diff --git a/docs/seqgra.html b/docs/seqgra.html
@@ -209,6 +209,21 @@
 
   <div class="section" id="module-seqgra">
 <span id="seqgra-package"></span><h1>seqgra package<a class="headerlink" href="#module-seqgra" title="Permalink to this headline">¶</a></h1>
+<p>seqgra schema and miscellaneous helper functions</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.AnnotatedExample" title="seqgra.schema.AnnotatedExample"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotatedExample</span></code></a>: (x, y, a) tuple - sequence window, label, annotation (data class)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.AnnotatedExampleSet" title="seqgra.schema.AnnotatedExampleSet"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotatedExampleSet</span></code></a>: (x, y, a) tuple - sequence windows, labels, annotations (named tuple)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.AnnotationSet" title="seqgra.schema.AnnotationSet"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationSet</span></code></a>: (y, a) tuple - labels, annotations (named tuple)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.Example" title="seqgra.schema.Example"><code class="xref py py-class docutils literal notranslate"><span class="pre">Example</span></code></a>: (x, y) tuple - sequence window, label (data class)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.ExampleSet" title="seqgra.schema.ExampleSet"><code class="xref py py-class docutils literal notranslate"><span class="pre">ExampleSet</span></code></a>: (x, y) tuple - sequence windows, labels (named tuple)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.Metrics" title="seqgra.schema.Metrics"><code class="xref py py-class docutils literal notranslate"><span class="pre">Metrics</span></code></a>: (loss, accuracy) tuple (named tuple)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.ModelSize" title="seqgra.schema.ModelSize"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModelSize</span></code></a>: (n1, n2) tuple - number of trainable parameters, number of non-trainable parameters (named tuple)</p></li>
+<li><p><a class="reference internal" href="seqgra.schema.html#seqgra.schema.ProbabilisticToken" title="seqgra.schema.ProbabilisticToken"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProbabilisticToken</span></code></a>: (t, p) tuple - token, probability (named tuple)</p></li>
+<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">MiscHelper</span></code>: miscellaneous helper functions</p></li>
+</ul>
+</dd>
+</dl>
 <div class="section" id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">

diff --git a/docs/seqgra.learner.bayes.html b/docs/seqgra.learner.bayes.html
@@ -212,6 +212,17 @@
 
   <div class="section" id="module-seqgra.learner.bayes">
 <span id="seqgra-learner-bayes-package"></span><h1>seqgra.learner.bayes package<a class="headerlink" href="#module-seqgra.learner.bayes" title="Permalink to this headline">¶</a></h1>
+<p>seqgra learner hierarchy - Bayes Optimal Classifier (BOC)</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="seqgra.learner.bayes.bayeslearner.html#seqgra.learner.bayes.bayeslearner.BayesOptimalDNAMultiClassClassificationLearner" title="seqgra.learner.bayes.bayeslearner.BayesOptimalDNAMultiClassClassificationLearner"><code class="xref py py-class docutils literal notranslate"><span class="pre">BayesOptimalDNAMultiClassClassificationLearner</span></code></a>: BOC implementation of DNA-based multi-class classification learner</p></li>
+<li><p><a class="reference internal" href="seqgra.learner.bayes.bayeslearner.html#seqgra.learner.bayes.bayeslearner.BayesOptimalDNAMultiLabelClassificationLearner" title="seqgra.learner.bayes.bayeslearner.BayesOptimalDNAMultiLabelClassificationLearner"><code class="xref py py-class docutils literal notranslate"><span class="pre">BayesOptimalDNAMultiLabelClassificationLearner</span></code></a>: BOC implementation of DNA-based multi-label classification learner</p></li>
+<li><p><a class="reference internal" href="seqgra.learner.bayes.bayeslearner.html#seqgra.learner.bayes.bayeslearner.BayesOptimalProteinMultiClassClassificationLearner" title="seqgra.learner.bayes.bayeslearner.BayesOptimalProteinMultiClassClassificationLearner"><code class="xref py py-class docutils literal notranslate"><span class="pre">BayesOptimalProteinMultiClassClassificationLearner</span></code></a>: BOC implementation of protein-based multi-class classification learner</p></li>
+<li><p><a class="reference internal" href="seqgra.learner.bayes.bayeslearner.html#seqgra.learner.bayes.bayeslearner.BayesOptimalProteinMultiLabelClassificationLearner" title="seqgra.learner.bayes.bayeslearner.BayesOptimalProteinMultiLabelClassificationLearner"><code class="xref py py-class docutils literal notranslate"><span class="pre">BayesOptimalProteinMultiLabelClassificationLearner</span></code></a>: BOC implementation of protein-based multi-label classification learner</p></li>
+<li><p><a class="reference internal" href="seqgra.learner.bayes.bayeshelper.html#seqgra.learner.bayes.bayeshelper.BayesOptimalHelper" title="seqgra.learner.bayes.bayeshelper.BayesOptimalHelper"><code class="xref py py-class docutils literal notranslate"><span class="pre">BayesOptimalHelper</span></code></a>: helper class for Bayes Optimal Classifier learners</p></li>
+</ul>
+</dd>
+</dl>
 <div class="section" id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">