Add axis_indices.

tanaylab · Jun 15, 2024 · a133c7f · a133c7f
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diff --git a/docs/v0.1.0/adapters.html b/docs/v0.1.0/adapters.html
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diff --git a/docs/v0.1.0/example_data.html b/docs/v0.1.0/example_data.html
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diff --git a/docs/v0.1.0/files_format.html b/docs/v0.1.0/files_format.html
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diff --git a/docs/v0.1.0/formats.html b/docs/v0.1.0/formats.html
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diff --git a/docs/v0.1.0/generic_functions.html b/docs/v0.1.0/generic_functions.html
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diff --git a/docs/v0.1.0/generic_locks.html b/docs/v0.1.0/generic_locks.html
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diff --git a/docs/v0.1.0/generic_logging.html b/docs/v0.1.0/generic_logging.html
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diff --git a/docs/v0.1.0/generic_types.html b/docs/v0.1.0/generic_types.html
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diff --git a/docs/v0.1.0/groups.html b/docs/v0.1.0/groups.html
@@ -428,7 +428,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/h5df_format.html b/docs/v0.1.0/h5df_format.html
@@ -749,7 +749,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/index.html b/docs/v0.1.0/index.html
@@ -1928,6 +1928,12 @@ <h1 id="Index">
 </a>
 </li>
 <li>
+<a href="readers.html#Daf.Readers.axis_indices">
+<code>Daf.Readers.axis_indices
+</code>
+</a>
+</li>
+<li>
 <a href="readers.html#Daf.Readers.axis_length">
 <code>Daf.Readers.axis_length
 </code>
@@ -2246,7 +2252,7 @@ <h1 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/matrix_layouts.html b/docs/v0.1.0/matrix_layouts.html
@@ -980,7 +980,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/memory_format.html b/docs/v0.1.0/memory_format.html
@@ -349,7 +349,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/messages.html b/docs/v0.1.0/messages.html
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diff --git a/docs/v0.1.0/objects.inv b/docs/v0.1.0/objects.inv
diff --git a/docs/v0.1.0/operations.html b/docs/v0.1.0/operations.html
@@ -1560,7 +1560,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/queries.html b/docs/v0.1.0/queries.html
@@ -4209,7 +4209,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/read_only.html b/docs/v0.1.0/read_only.html
@@ -543,7 +543,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/readers.html b/docs/v0.1.0/readers.html
@@ -641,6 +641,28 @@ <h1 id="Readers-axes">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
+<a class="docstring-binding" id="Daf.Readers.axis_indices" href="#Daf.Readers.axis_indices">
+<code>Daf.Readers.axis_indices
+</code>
+</a> — 
+<span class="docstring-category">Function
+</span>
+</header>
+<section>
+<div>
+<pre>
+<code class="language-julia hljs">function axis_indices(daf::DafReader, axis::AbstractString, entries::AbstractVector{&lt;:AbstractString})::AbstractVector{&lt;:Integer}
+</code>
+</pre>
+<p>Return a vector of the indices of the entries in the axis.
+</p>
+</div>
+</section>
+</article>
+<article class="docstring">
+<header>
+<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
+</a>
 <a class="docstring-binding" id="Daf.Readers.axis_length" href="#Daf.Readers.axis_length">
 <code>Daf.Readers.axis_length
 </code>
@@ -1213,6 +1235,12 @@ <h2 id="Index">
 </a>
 </li>
 <li>
+<a href="readers.html#Daf.Readers.axis_indices">
+<code>Daf.Readers.axis_indices
+</code>
+</a>
+</li>
+<li>
 <a href="readers.html#Daf.Readers.axis_length">
 <code>Daf.Readers.axis_length
 </code>
@@ -1347,7 +1375,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
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+</a> version 1.4.1. Using Julia version 1.10.4.
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diff --git a/docs/v0.1.0/reconstruction.html b/docs/v0.1.0/reconstruction.html
@@ -439,7 +439,7 @@ <h2 id="Index">
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diff --git a/docs/v0.1.0/registry.html b/docs/v0.1.0/registry.html
@@ -718,7 +718,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/search_index.js b/docs/v0.1.0/search_index.js
diff --git a/docs/v0.1.0/storage_types.html b/docs/v0.1.0/storage_types.html
@@ -695,7 +695,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/tokens.html b/docs/v0.1.0/tokens.html
@@ -900,7 +900,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/views.html b/docs/v0.1.0/views.html
@@ -944,7 +944,7 @@ <h2 id="Index">
 <hr/>
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diff --git a/docs/v0.1.0/writers.html b/docs/v0.1.0/writers.html
@@ -1294,7 +1294,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
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diff --git a/src/readers.jl b/src/readers.jl
@@ -36,6 +36,7 @@ module Readers
 export axes_set
 export axis_array
 export axis_dict
+export axis_indices
 export axis_length
 export axis_version_counter
 export description
@@ -241,6 +242,25 @@ function axis_dict(daf::DafReader, axis::AbstractString)::AbstractDict{<:Abstrac
     end
 end
 
+"""
+    function axis_indices(daf::DafReader, axis::AbstractString, entries::AbstractVector{<:AbstractString})::AbstractVector{<:Integer}
+
+Return a vector of the indices of the entries in the axis.
+"""
+function axis_indices(
+    daf::DafReader,
+    axis::AbstractString,
+    entries::AbstractVector{<:AbstractString},
+)::AbstractVector{<:Integer}
+    return Formats.with_data_read_lock(daf, "axis_indices of:", axis) do
+        require_axis(daf, "for: axis_indices", axis)
+        dictionary = Formats.axis_dict_with_cache(daf, axis)
+        result = getindex.(Ref(dictionary), entries)
+        @debug "axis_indices daf: $(depict(daf)) result: $(depict(result))"
+        return result
+    end
+end
+
 """
     axis_length(daf::DafReader, axis::AbstractString)::Int64
 

diff --git a/src/readers.md b/src/readers.md
@@ -20,6 +20,7 @@ Daf.Readers.has_axis
 Daf.Readers.axes_set
 Daf.Readers.axis_array
 Daf.Readers.axis_dict
+Daf.Readers.axis_indices
 Daf.Readers.axis_length
 ```
 

diff --git a/test/data.jl b/test/data.jl
@@ -357,6 +357,11 @@ function test_existing_axis(daf::DafReader, depth::Int)::Nothing
         @test collect(axis_dict(daf, "cell")) == [name => index for (index, name) in enumerate(CELL_NAMES)]
     end
 
+    nested_test("axis_indices") do
+        @test axis_indices(daf, "gene", GENE_NAMES) == collect(1:length(GENE_NAMES))
+        @test axis_indices(daf, "cell", reverse(CELL_NAMES)) == collect(reverse(1:length(CELL_NAMES)))
+    end
+
     nested_test("name") do
         @test get_vector(daf, "gene", "name") == GENE_NAMES
         @test get_vector(daf, "cell", "name") == CELL_NAMES