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_modules/index.html

@@ -248,6 +248,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="rds2py/lib_rds_parser.html">rds2py.lib_rds_parser</a></li>
 <li><a href="rds2py/rdsutils.html">rds2py.rdsutils</a></li>
 <li><a href="rds2py/read_atomic.html">rds2py.read_atomic</a></li>
+<li><a href="rds2py/read_delayed_matrix.html">rds2py.read_delayed_matrix</a></li>
 <li><a href="rds2py/read_dict.html">rds2py.read_dict</a></li>
 <li><a href="rds2py/read_factor.html">rds2py.read_factor</a></li>
 <li><a href="rds2py/read_frame.html">rds2py.read_frame</a></li>

_modules/rds2py/generics.html

@@ -303,6 +303,8 @@ <h1>Source code for rds2py.generics</h1><div class="highlight"><pre>
     <span class="c1"># multi assay experiment</span>
     <span class="s2">&quot;MultiAssayExperiment&quot;</span><span class="p">:</span> <span class="s2">&quot;rds2py.read_mae.read_multi_assay_experiment&quot;</span><span class="p">,</span>
     <span class="s2">&quot;ExperimentList&quot;</span><span class="p">:</span> <span class="s2">&quot;rds2py.read_dict.read_dict&quot;</span><span class="p">,</span>
+    <span class="c1"># delayed matrices</span>
+    <span class="s2">&quot;H5SparseMatrix&quot;</span><span class="p">:</span> <span class="s2">&quot;rds2py.read_delayed_matrix.read_hdf5_sparse&quot;</span><span class="p">,</span>
 <span class="p">}</span>
 
 

_sources/api/rds2py.rst.txt

@@ -44,6 +44,14 @@ rds2py.read\_atomic module
    :undoc-members:
    :show-inheritance:
 
+rds2py.read\_delayed\_matrix module
+-----------------------------------
+
+.. automodule:: rds2py.read_delayed_matrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 rds2py.read\_dict module
 ------------------------
 

api/modules.html

@@ -306,6 +306,10 @@ <h1>rds2py<a class="headerlink" href="#rds2py" title="Link to this heading">¶</
 <li class="toctree-l3"><a class="reference internal" href="rds2py.html#rds2py.read_atomic.read_string_vector"><code class="docutils literal notranslate"><span class="pre">read_string_vector()</span></code></a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="rds2py.html#module-rds2py.read_delayed_matrix">rds2py.read_delayed_matrix module</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="rds2py.html#rds2py.read_delayed_matrix.read_hdf5_sparse"><code class="docutils literal notranslate"><span class="pre">read_hdf5_sparse()</span></code></a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="rds2py.html#module-rds2py.read_dict">rds2py.read_dict module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="rds2py.html#rds2py.read_dict.read_dict"><code class="docutils literal notranslate"><span class="pre">read_dict()</span></code></a></li>
 </ul>

api/rds2py.html

@@ -567,6 +567,27 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </dl>
 </dd></dl>
 
+</section>
+<section id="module-rds2py.read_delayed_matrix">
+<span id="rds2py-read-delayed-matrix-module"></span><h2>rds2py.read_delayed_matrix module<a class="headerlink" href="#module-rds2py.read_delayed_matrix" title="Link to this heading">¶</a></h2>
+<p>Functions and classes for parsing R delayed matrix objects from HDF5Array.</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="rds2py.read_delayed_matrix.read_hdf5_sparse">
+<span class="sig-prename descclassname"><span class="pre">rds2py.read_delayed_matrix.</span></span><span class="sig-name descname"><span class="pre">read_hdf5_sparse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">robject</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.9/library/stdtypes.html#dict" title="(in Python v3.9)"><span class="pre">dict</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Hdf5CompressedSparseMatrix</span></span></span><a class="reference internal" href="../_modules/rds2py/read_delayed_matrix.html#read_hdf5_sparse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#rds2py.read_delayed_matrix.read_hdf5_sparse" title="Link to this definition">¶</a></dt>
+<dd><p>Convert an R delayed sparse array (H5-backed).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>robject</strong> – Dictionary containing parsed delayed sparse array.</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A Hdf5CompressedSparseMatrix from the ‘hdf5array’ package.</p>
+</dd>
+</dl>
+</dd></dl>
+
 </section>
 <section id="module-rds2py.read_dict">
 <span id="rds2py-read-dict-module"></span><h2>rds2py.read_dict module<a class="headerlink" href="#module-rds2py.read_dict" title="Link to this heading">¶</a></h2>
@@ -1033,6 +1054,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li><a class="reference internal" href="#rds2py.read_atomic.read_string_vector"><code class="docutils literal notranslate"><span class="pre">read_string_vector()</span></code></a></li>
 </ul>
 </li>
+<li><a class="reference internal" href="#module-rds2py.read_delayed_matrix">rds2py.read_delayed_matrix module</a><ul>
+<li><a class="reference internal" href="#rds2py.read_delayed_matrix.read_hdf5_sparse"><code class="docutils literal notranslate"><span class="pre">read_hdf5_sparse()</span></code></a></li>
+</ul>
+</li>
 <li><a class="reference internal" href="#module-rds2py.read_dict">rds2py.read_dict module</a><ul>
 <li><a class="reference internal" href="#rds2py.read_dict.read_dict"><code class="docutils literal notranslate"><span class="pre">read_dict()</span></code></a></li>
 </ul>

changelog.html

@@ -251,6 +251,12 @@
         <article role="main" id="furo-main-content">
           <section class="tex2jax_ignore mathjax_ignore" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading">¶</a></h1>
+<section id="version-0-5-1">
+<h2>Version 0.5.1<a class="headerlink" href="#version-0-5-1" title="Link to this heading">¶</a></h2>
+<ul class="simple">
+<li><p>Added parser for delayed sparse objects backed by H5</p></li>
+</ul>
+</section>
 <section id="version-0-5-0">
 <h2>Version 0.5.0<a class="headerlink" href="#version-0-5-0" title="Link to this heading">¶</a></h2>
 <ul class="simple">
@@ -354,6 +360,7 @@ <h2>Version 0.1<a class="headerlink" href="#version-0-1" title="Link to this hea
           <div class="toc-tree">
             <ul>
 <li><a class="reference internal" href="#">Changelog</a><ul>
+<li><a class="reference internal" href="#version-0-5-1">Version 0.5.1</a></li>
 <li><a class="reference internal" href="#version-0-5-0">Version 0.5.0</a></li>
 <li><a class="reference internal" href="#version-0-4-5">Version 0.4.5</a></li>
 <li><a class="reference internal" href="#version-0-4-4">Version 0.4.4</a></li>

genindex.html

@@ -337,6 +337,8 @@ <h2>M</h2>
           <li><a href="api/rds2py.html#module-rds2py.rdsutils">rds2py.rdsutils</a>
 </li>
           <li><a href="api/rds2py.html#module-rds2py.read_atomic">rds2py.read_atomic</a>
+</li>
+          <li><a href="api/rds2py.html#module-rds2py.read_delayed_matrix">rds2py.read_delayed_matrix</a>
 </li>
           <li><a href="api/rds2py.html#module-rds2py.read_dict">rds2py.read_dict</a>
 </li>
@@ -425,6 +427,13 @@ <h2>R</h2>
 
         <ul>
           <li><a href="api/rds2py.html#module-rds2py.read_atomic">module</a>
+</li>
+        </ul></li>
+        <li>
+    rds2py.read_delayed_matrix
+
+        <ul>
+          <li><a href="api/rds2py.html#module-rds2py.read_delayed_matrix">module</a>
 </li>
         </ul></li>
         <li>
@@ -523,6 +532,8 @@ <h2>R</h2>
         <li><a href="api/rds2py.html#rds2py.read_granges.read_genomic_ranges">read_genomic_ranges() (in module rds2py.read_granges)</a>
 </li>
         <li><a href="api/rds2py.html#rds2py.read_granges.read_granges_list">read_granges_list() (in module rds2py.read_granges)</a>
+</li>
+        <li><a href="api/rds2py.html#rds2py.read_delayed_matrix.read_hdf5_sparse">read_hdf5_sparse() (in module rds2py.read_delayed_matrix)</a>
 </li>
         <li><a href="api/rds2py.html#rds2py.read_atomic.read_integer_vector">read_integer_vector() (in module rds2py.read_atomic)</a>
 </li>

index.html

@@ -266,7 +266,6 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme.html">Overview</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="readme.html#installation">Installation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme.html#quick-start">Quick Start</a></li>
 <li class="toctree-l2"><a class="reference internal" href="readme.html#usage">Usage</a></li>
 <li class="toctree-l2"><a class="reference internal" href="readme.html#write-your-own-reader">Write-your-own-reader</a></li>
 <li class="toctree-l2"><a class="reference internal" href="readme.html#type-conversion-reference">Type Conversion Reference</a></li>
@@ -290,6 +289,7 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 <li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="authors.html">Authors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-5-1">Version 0.5.1</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-5-0">Version 0.5.0</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-4-5">Version 0.4.5</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-0-4-4">Version 0.4.4</a></li>

py-modindex.html

@@ -290,6 +290,12 @@ <h1>Python Module Index</h1>
         <a href="api/rds2py.html#module-rds2py.read_atomic"><code class="xref">rds2py.read_atomic</code></a></td><td>
     <em></em></td>
   </tr>
+  <tr class="cg-1">
+    <td></td>
+    <td>&#160;&#160;&#160;
+        <a href="api/rds2py.html#module-rds2py.read_delayed_matrix"><code class="xref">rds2py.read_delayed_matrix</code></a></td><td>
+    <em></em></td>
+  </tr>
   <tr class="cg-1">
     <td></td>
     <td>&#160;&#160;&#160;

readme.html

@@ -298,15 +298,9 @@ <h1>rds2py<a class="headerlink" href="#rds2py" title="Link to this heading">¶</
 <h2>Installation<a class="headerlink" href="#installation" title="Link to this heading">¶</a></h2>
 <p>Package is published to <a class="reference external" href="https://pypi.org/project/rds2py/">PyPI</a></p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>rds2py
-</pre></div>
-</div>
-</section>
-<section id="quick-start">
-<h2>Quick Start<a class="headerlink" href="#quick-start" title="Link to this heading">¶</a></h2>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">rds2py</span> <span class="kn">import</span> <span class="n">read_rds</span>
 
-<span class="c1"># Read any RDS file</span>
-<span class="n">r_obj</span> <span class="o">=</span> <span class="n">read_rds</span><span class="p">(</span><span class="s2">&quot;path/to/file.rds&quot;</span><span class="p">)</span>
+<span class="c1"># or install optional dependencies</span>
+pip<span class="w"> </span>install<span class="w"> </span>rds2py<span class="o">[</span>optional<span class="o">]</span>
 </pre></div>
 </div>
 </section>
@@ -448,7 +442,6 @@ <h2>Note<a class="headerlink" href="#note" title="Link to this heading">¶</a></
             <ul>
 <li><a class="reference internal" href="#">rds2py</a><ul>
 <li><a class="reference internal" href="#installation">Installation</a></li>
-<li><a class="reference internal" href="#quick-start">Quick Start</a></li>
 <li><a class="reference internal" href="#usage">Usage</a><ul>
 <li><a class="reference internal" href="#basic-usage">Basic Usage</a></li>
 </ul>