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| <h1>Source code for bed_reader._sample_data</h1><div class="highlight"><pre> | ||
| <span></span><span class="kn">import</span> <span class="nn">tempfile</span> | ||
| <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span> | ||
| <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span> | ||
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| <span class="k">try</span><span class="p">:</span> | ||
| <span class="kn">import</span> <span class="nn">pooch</span> | ||
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| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Load sample data.</span> | ||
| <span class="sd"> """</span> | ||
|
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||
| <span class="n">POOCH</span> <span class="o">=</span> <span class="n">pooch</span><span class="o">.</span><span class="n">create</span><span class="p">(</span> | ||
| <span class="c1"># Use the default cache folder for the OS</span> | ||
| <span class="n">path</span><span class="o">=</span><span class="n">pooch</span><span class="o">.</span><span class="n">os_cache</span><span class="p">(</span><span class="s2">"bed_reader"</span><span class="p">),</span> | ||
| <span class="c1"># The remote data is on Github</span> | ||
| <span class="n">base_url</span><span class="o">=</span><span class="s2">"https://raw.githubusercontent.com/"</span> | ||
| <span class="o">+</span> <span class="s2">"fastlmm/bed-reader/Oct2023/bed_reader/tests/data/"</span><span class="p">,</span> | ||
| <span class="c1"># If this is a development version, get the data from the master branch</span> | ||
| <span class="n">version_dev</span><span class="o">=</span><span class="s2">"master"</span><span class="p">,</span> | ||
| <span class="c1"># The registry specifies the files that can be fetched</span> | ||
| <span class="n">env</span><span class="o">=</span><span class="s2">"BED_READER_DATA_DIR"</span><span class="p">,</span> | ||
| <span class="p">)</span> | ||
|
|
||
| <span class="c1"># Get registry file from package_data</span> | ||
| <span class="n">registry_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s2">"tests/registry.txt"</span> | ||
| <span class="c1"># Load this registry file</span> | ||
| <span class="n">POOCH</span><span class="o">.</span><span class="n">load_registry</span><span class="p">(</span><span class="n">registry_file</span><span class="p">)</span> | ||
| <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span> | ||
| <span class="n">pooch</span> <span class="o">=</span> <span class="kc">None</span> | ||
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| <div class="viewcode-block" id="sample_file"><a class="viewcode-back" href="../../index.html#bed_reader.sample_file">[docs]</a><span class="k">def</span> <span class="nf">sample_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Path</span><span class="p">])</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).</span> | ||
|
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||
| <span class="sd"> Parameters</span> | ||
| <span class="sd"> ----------</span> | ||
| <span class="sd"> filepath</span> | ||
| <span class="sd"> Name of the sample .bed file.</span> | ||
|
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||
| <span class="sd"> Returns</span> | ||
| <span class="sd"> -------</span> | ||
| <span class="sd"> str</span> | ||
| <span class="sd"> Local name of sample .bed file.</span> | ||
|
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||
|
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||
| <span class="sd"> By default this function puts files under the user's cache directory.</span> | ||
| <span class="sd"> Override this by setting</span> | ||
| <span class="sd"> the `BED_READER_DATA_DIR` environment variable.</span> | ||
|
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| <span class="sd"> Example</span> | ||
| <span class="sd"> --------</span> | ||
|
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||
| <span class="sd"> .. doctest::</span> | ||
|
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| <span class="sd"> >>> # pip install bed-reader[samples] # if needed</span> | ||
| <span class="sd"> >>> from bed_reader import sample_file</span> | ||
| <span class="sd"> >>></span> | ||
| <span class="sd"> >>> file_name = sample_file("small.bed")</span> | ||
| <span class="sd"> >>> print(f"The local file name is '{file_name}'")</span> | ||
| <span class="sd"> The local file name is '...small.bed'</span> | ||
| <span class="sd"> """</span> | ||
| <span class="k">if</span> <span class="n">pooch</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> | ||
| <span class="k">raise</span> <span class="ne">ImportError</span><span class="p">(</span> | ||
| <span class="s2">"The function sample_file() requires pooch. "</span> | ||
| <span class="o">+</span> <span class="s2">"Install it with 'pip install --upgrade bed-reader[sample]'."</span> | ||
| <span class="p">)</span> | ||
|
|
||
| <span class="n">filepath</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">filepath</span><span class="p">)</span> | ||
| <span class="n">file_string</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">filepath</span><span class="p">)</span> | ||
| <span class="k">if</span> <span class="n">file_string</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">".bed"</span><span class="p">):</span> | ||
| <span class="n">POOCH</span><span class="o">.</span><span class="n">fetch</span><span class="p">(</span><span class="n">file_string</span><span class="p">[:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span> <span class="o">+</span> <span class="s2">".fam"</span><span class="p">)</span> | ||
| <span class="n">POOCH</span><span class="o">.</span><span class="n">fetch</span><span class="p">(</span><span class="n">file_string</span><span class="p">[:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span> <span class="o">+</span> <span class="s2">".bim"</span><span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">POOCH</span><span class="o">.</span><span class="n">fetch</span><span class="p">(</span><span class="n">file_string</span><span class="p">)</span></div> | ||
|
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|
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| <div class="viewcode-block" id="tmp_path"><a class="viewcode-back" href="../../index.html#bed_reader.tmp_path">[docs]</a><span class="k">def</span> <span class="nf">tmp_path</span><span class="p">()</span> <span class="o">-></span> <span class="n">Path</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Return a :class:`pathlib.Path` to a temporary directory.</span> | ||
|
|
||
| <span class="sd"> Returns</span> | ||
| <span class="sd"> -------</span> | ||
| <span class="sd"> pathlib.Path</span> | ||
| <span class="sd"> a temporary directory</span> | ||
|
|
||
| <span class="sd"> Example</span> | ||
| <span class="sd"> --------</span> | ||
|
|
||
| <span class="sd"> .. doctest::</span> | ||
|
|
||
| <span class="sd"> >>> from bed_reader import to_bed, tmp_path</span> | ||
| <span class="sd"> >>></span> | ||
| <span class="sd"> >>> output_file = tmp_path() / "small3.bed"</span> | ||
| <span class="sd"> >>> val = [[1, 0, -127, 0], [2, 0, -127, 2], [0, 1, 2, 0]]</span> | ||
| <span class="sd"> >>> to_bed(output_file, val)</span> | ||
|
|
||
| <span class="sd"> """</span> | ||
| <span class="n">temp_dir</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">()</span> | ||
| <span class="n">path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">)</span> <span class="o">/</span> <span class="s2">"bed_reader_tmp_path"</span> | ||
| <span class="n">path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">path</span></div> | ||
|
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||
|
|
||
| <span class="c1"># if __name__ == "__main__":</span> | ||
| <span class="c1"># logging.basicConfig(level=logging.INFO)</span> | ||
|
|
||
| <span class="c1"># import pytest</span> | ||
|
|
||
| <span class="c1"># pytest.main(["--doctest-modules", __file__])</span> | ||
| </pre></div> | ||
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