Convert to and from h5ad.

tanaylab · Mar 23, 2024 · 7a584a7 · 7a584a7
1 parent 10273a5
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diff --git a/daf/__init__.py b/daf/__init__.py
@@ -51,6 +51,7 @@
 # pylint: disable=wildcard-import,unused-wildcard-import
 
 from .julia_import import *  # isort: skip
+from .generic import *  # isort: skip
 from .storage_types import *  # isort: skip
 from .operations import *  # isort: skip
 from .queries import *  # isort: skip
@@ -60,3 +61,4 @@
 from .copies import *  # isort: skip
 from .adapters import *  # isort: skip
 from .concat import *  # isort: skip
+from .anndata_format import *  # isort: skip
diff --git a/daf/anndata_format.py b/daf/anndata_format.py
@@ -0,0 +1,56 @@
+"""
+Import/export ``Daf`` data from/to ``AnnData``. See the Julia
+`documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html>`__ for details.
+"""
+
+__all__ = ["h5ad_as_daf", "daf_as_h5ad"]
+
+from typing import Optional
+
+from .data import DafReader
+from .formats import MemoryDaf
+from .generic import JL_ABNORMAL_HANDLER
+from .generic import AbnormalHandler
+from .julia_import import jl
+
+
+def h5ad_as_daf(
+    h5ad: str,
+    *,
+    name: Optional[str] = None,
+    obs_is: Optional[str] = None,
+    var_is: Optional[str] = None,
+    X_is: Optional[str] = None,
+    unsupported_handler: AbnormalHandler = "WarnHandler",
+) -> MemoryDaf:
+    """
+    View ``AnnData`` as a ``Daf`` data set, specifically using a ``MemoryDaf``. See the Julia
+    `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#anndata_as_daf>`__ for details.
+
+    Note that you only pass an ``h5ad`` path, since the Julia ``AnnData`` object comes from the ``Muon.jl`` package and
+    is not compatible with the Python ``anndata`` object.
+    """
+    return MemoryDaf(
+        jl.Daf.anndata_as_daf(
+            h5ad,
+            name=name,
+            obs_is=obs_is,
+            var_is=var_is,
+            X_is=X_is,
+            unsupported_handler=JL_ABNORMAL_HANDLER[unsupported_handler],
+        )
+    )
+
+
+def daf_as_h5ad(
+    daf: DafReader, *, obs_is: Optional[str] = None, var_is: Optional[str] = None, X_is: Optional[str] = None, h5ad: str
+) -> None:
+    """
+    View the ``Daf`` data set as ``AnnData``. See the Julia
+    `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#Daf.AnnDataFormat.daf_as_anndata>`__
+    for details.
+
+    Note this just creates the ``h5ad`` file. We do not return the ``AnnData`` object, because it is a Julia
+    (``Muon.jl``) ``AnnData`` object, which is **not** a Python ``anndata`` ``AnnData`` object.
+    """
+    jl.daf_as_anndata(daf, obs_is=obs_is, var_is=var_is, X_is=X_is, h5ad=h5ad)
diff --git a/daf/formats.py b/daf/formats.py
@@ -20,8 +20,10 @@ class MemoryDaf(DafWriter):
     `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/memory_format.html>`__ for details.
     """
 
-    def __init__(self, *, name: str = "memory") -> None:
-        super().__init__(jl.Daf.MemoryDaf(name=name))
+    def __init__(self, jl_obj: Optional[jl.MemoryDaf] = None, *, name: str = "memory") -> None:
+        if jl_obj is None:
+            jl_obj = jl.Daf.MemoryDaf(name=name)
+        super().__init__(jl_obj)
 
 
 class FilesDaf(DafWriter):

diff --git a/daf/generic.py b/daf/generic.py
@@ -0,0 +1,21 @@
+"""
+Types that arguably should belong in a more general-purpose package. See the Julia
+`documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/generic.html>`__ for details.
+"""
+
+from typing import Literal
+
+from .julia_import import jl
+
+__all__ = ["AbnormalHandler"]
+
+
+#: The action to take when encountering an "abnormal" (but recoverable) operation. See the Julia
+#: `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/generic.html#Daf.Generic.AbnormalHandler>`__ for details.
+AbnormalHandler = Literal["IgnoreHandler"] | Literal["WarnHandler"] | Literal["ErrorHandler"]
+
+JL_ABNORMAL_HANDLER = {
+    "IgnoreHandler": jl.Daf.Generic.IgnoreHandler,
+    "WarnHandler": jl.Daf.Generic.WarnHandler,
+    "ErrorHandler": jl.Daf.Generic.ErrorHandler,
+}
diff --git a/daf/julia_import.py b/daf/julia_import.py
@@ -85,9 +85,10 @@
 jl.seval("import DataFrames")
 jl.seval("import HDF5")
 jl.seval("import LinearAlgebra")
+jl.seval("import Muon")
 jl.seval("import NamedArrays")
-jl.seval("import SparseArrays")
 jl.seval("import PythonCall")
+jl.seval("import SparseArrays")
 
 
 class UndefInitializer:

diff --git a/docs/API.rst b/docs/API.rst
@@ -7,11 +7,13 @@ API
 
   julia_import
   data
+  storage_types
   queries
   operations
   formats
   views
   copies
   adapters
   concat
-  storage_types
+  anndata_format
+  generic
diff --git a/docs/anndata_format.rst b/docs/anndata_format.rst
@@ -0,0 +1,5 @@
+anndata_format
+==============
+
+.. automodule:: daf.anndata_format
+    :Members:
diff --git a/docs/v0.1.0/html/API.html b/docs/v0.1.0/html/API.html
@@ -125,6 +125,11 @@
 </a>
 </li>
 
+<li class="toctree-l2">
+<a class="reference internal" href="storage_types.html">storage_types
+</a>
+</li>
+
 <li class="toctree-l2">
 <a class="reference internal" href="queries.html">queries
 </a>
@@ -161,7 +166,7 @@
 </li>
 
 <li class="toctree-l2">
-<a class="reference internal" href="storage_types.html">storage_types
+<a class="reference internal" href="anndata_format.html">anndata_format
 </a>
 </li>
 
@@ -898,6 +903,33 @@ <h1>API
 
 </li>
 
+<li class="toctree-l1">
+<a class="reference internal" href="storage_types.html">storage_types
+</a>
+<ul>
+
+<li class="toctree-l2">
+<a class="reference internal" href="storage_types.html#daf.storage_types.StorageNumber">
+<code class="docutils literal notranslate">
+<span class="pre">StorageNumber
+</span>
+</code>
+</a>
+</li>
+
+<li class="toctree-l2">
+<a class="reference internal" href="storage_types.html#daf.storage_types.StorageScalar">
+<code class="docutils literal notranslate">
+<span class="pre">StorageScalar
+</span>
+</code>
+</a>
+</li>
+
+</ul>
+
+</li>
+
 <li class="toctree-l1">
 <a class="reference internal" href="queries.html">queries
 </a>
@@ -1565,23 +1597,23 @@ <h1>API
 </li>
 
 <li class="toctree-l1">
-<a class="reference internal" href="storage_types.html">storage_types
+<a class="reference internal" href="anndata_format.html">anndata_format
 </a>
 <ul>
 
 <li class="toctree-l2">
-<a class="reference internal" href="storage_types.html#daf.storage_types.StorageNumber">
+<a class="reference internal" href="anndata_format.html#daf.anndata_format.h5ad_as_daf">
 <code class="docutils literal notranslate">
-<span class="pre">StorageNumber
+<span class="pre">h5ad_as_daf()
 </span>
 </code>
 </a>
 </li>
 
 <li class="toctree-l2">
-<a class="reference internal" href="storage_types.html#daf.storage_types.StorageScalar">
+<a class="reference internal" href="anndata_format.html#daf.anndata_format.daf_as_h5ad">
 <code class="docutils literal notranslate">
-<span class="pre">StorageScalar
+<span class="pre">daf_as_h5ad()
 </span>
 </code>
 </a>

diff --git a/docs/v0.1.0/html/_modules/daf/anndata_format.html b/docs/v0.1.0/html/_modules/daf/anndata_format.html
@@ -0,0 +1,171 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>daf.anndata_format &mdash; Daf 0.1.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
+
+
+  <!--[if lt IE 9]>
+    <script src="../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <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=01f34227"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../../index.html" class="icon icon-home">
+            Daf
+              <img src="../../_static/logo.svg" class="logo" alt="Logo"/>
+          </a>
+              <div class="version">
+                0.1.0
+              </div>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="../../readme.html">README</a></li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../API.html">API</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../../index.html">Daf</a>
+      </nav>
+
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+          <div role="navigation" aria-label="Page navigation">
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+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">daf.anndata_format</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>Source code for daf.anndata_format</h1><div class="highlight"><pre>
+<span></span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Import/export ``Daf`` data from/to ``AnnData``. See the Julia</span>
+<span class="sd">`documentation &lt;https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html&gt;`__ for details.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;h5ad_as_daf&quot;</span><span class="p">,</span> <span class="s2">&quot;daf_as_h5ad&quot;</span><span class="p">]</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span>
+
+<span class="kn">from</span> <span class="nn">.data</span> <span class="kn">import</span> <span class="n">DafReader</span>
+<span class="kn">from</span> <span class="nn">.formats</span> <span class="kn">import</span> <span class="n">MemoryDaf</span>
+<span class="kn">from</span> <span class="nn">.generic</span> <span class="kn">import</span> <span class="n">JL_ABNORMAL_HANDLER</span>
+<span class="kn">from</span> <span class="nn">.generic</span> <span class="kn">import</span> <span class="n">AbnormalHandler</span>
+<span class="kn">from</span> <span class="nn">.julia_import</span> <span class="kn">import</span> <span class="n">jl</span>
+
+
+<div class="viewcode-block" id="h5ad_as_daf">
+<a class="viewcode-back" href="../../anndata_format.html#daf.anndata_format.h5ad_as_daf">[docs]</a>
+<span class="k">def</span> <span class="nf">h5ad_as_daf</span><span class="p">(</span>
+    <span class="n">h5ad</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="o">*</span><span class="p">,</span>
+    <span class="n">name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">obs_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">var_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">X_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">unsupported_handler</span><span class="p">:</span> <span class="n">AbnormalHandler</span> <span class="o">=</span> <span class="s2">&quot;WarnHandler&quot;</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">MemoryDaf</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    View ``AnnData`` as a ``Daf`` data set, specifically using a ``MemoryDaf``. See the Julia</span>
+<span class="sd">    `documentation &lt;https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#anndata_as_daf&gt;`__ for details.</span>
+
+<span class="sd">    Note that you only pass an ``h5ad`` path, since the Julia ``AnnData`` object comes from the ``Muon.jl`` package and</span>
+<span class="sd">    is not compatible with the Python ``anndata`` object.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">MemoryDaf</span><span class="p">(</span>
+        <span class="n">jl</span><span class="o">.</span><span class="n">Daf</span><span class="o">.</span><span class="n">anndata_as_daf</span><span class="p">(</span>
+            <span class="n">h5ad</span><span class="p">,</span>
+            <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">obs_is</span><span class="o">=</span><span class="n">obs_is</span><span class="p">,</span>
+            <span class="n">var_is</span><span class="o">=</span><span class="n">var_is</span><span class="p">,</span>
+            <span class="n">X_is</span><span class="o">=</span><span class="n">X_is</span><span class="p">,</span>
+            <span class="n">unsupported_handler</span><span class="o">=</span><span class="n">JL_ABNORMAL_HANDLER</span><span class="p">[</span><span class="n">unsupported_handler</span><span class="p">],</span>
+        <span class="p">)</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="daf_as_h5ad">
+<a class="viewcode-back" href="../../anndata_format.html#daf.anndata_format.daf_as_h5ad">[docs]</a>
+<span class="k">def</span> <span class="nf">daf_as_h5ad</span><span class="p">(</span>
+    <span class="n">daf</span><span class="p">:</span> <span class="n">DafReader</span><span class="p">,</span> <span class="o">*</span><span class="p">,</span> <span class="n">obs_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">var_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">X_is</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">h5ad</span><span class="p">:</span> <span class="nb">str</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    View the ``Daf`` data set as ``AnnData``. See the Julia</span>
+<span class="sd">    `documentation &lt;https://tanaylab.github.io/Daf.jl/v0.1.0/anndata_format.html#Daf.AnnDataFormat.daf_as_anndata&gt;`__</span>
+<span class="sd">    for details.</span>
+
+<span class="sd">    Note this just creates the ``h5ad`` file. We do not return the ``AnnData`` object, because it is a Julia</span>
+<span class="sd">    (``Muon.jl``) ``AnnData`` object, which is **not** a Python ``anndata`` ``AnnData`` object.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">jl</span><span class="o">.</span><span class="n">daf_as_anndata</span><span class="p">(</span><span class="n">daf</span><span class="p">,</span> <span class="n">obs_is</span><span class="o">=</span><span class="n">obs_is</span><span class="p">,</span> <span class="n">var_is</span><span class="o">=</span><span class="n">var_is</span><span class="p">,</span> <span class="n">X_is</span><span class="o">=</span><span class="n">X_is</span><span class="p">,</span> <span class="n">h5ad</span><span class="o">=</span><span class="n">h5ad</span><span class="p">)</span></div>
+
+</pre></div>
+
+           </div>
+          </div>
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