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<div class="section" id="api"> |
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<h1>API<a class="headerlink" href="#api" title="Permalink to this headline">¶</a></h1> |
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<li class="toctree-l1"><a class="reference internal" href="dscript.commands.html">dscript.commands</a><ul> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-embed">dscript.commands.embed</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-predict">dscript.commands.predict</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.models.html#dscript-models-embedding">dscript.models.embedding</a></li> |
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<div class="section" id="dscript-alphabets"> |
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<h2>dscript.alphabets<a class="headerlink" href="#dscript-alphabets" title="Permalink to this headline">¶</a></h2> |
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</div> |
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<div class="section" id="module-dscript.fasta"> |
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<span id="dscript-fasta"></span><h2>dscript.fasta<a class="headerlink" href="#module-dscript.fasta" title="Permalink to this headline">¶</a></h2> |
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<dl class="py function"> |
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<dt id="dscript.fasta.parse"> |
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<code class="sig-prename descclassname">dscript.fasta.</code><code class="sig-name descname">parse</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">f</span></em>, <em class="sig-param"><span class="n">comment</span><span class="o">=</span><span class="default_value">'#'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#dscript.fasta.parse" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Parse a file in <code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
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<li><p><strong>f</strong> (<em>_io.TextIOWrapper</em>) – Input file object</p></li> |
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<li><p><strong>comment</strong> (<em>str</em>) – Character used for comments</p></li> |
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</ul> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>names, sequence</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>list[str], list[str]</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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<dl class="py function"> |
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<dt id="dscript.fasta.parse_directory"> |
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<code class="sig-prename descclassname">dscript.fasta.</code><code class="sig-name descname">parse_directory</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">directory</span></em>, <em class="sig-param"><span class="n">extension</span><span class="o">=</span><span class="default_value">'.seq'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#parse_directory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#dscript.fasta.parse_directory" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Parse all files in a directory ending with <code class="docutils literal notranslate"><span class="pre">extension</span></code>.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
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<li><p><strong>directory</strong> (<em>str</em>) – Input directory</p></li> |
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<li><p><strong>extension</strong> (<em>str</em>) – Extension of all files to read in</p></li> |
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</ul> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>names, sequence</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>list[str], list[str]</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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<dl class="py function"> |
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<dt id="dscript.fasta.write"> |
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<code class="sig-prename descclassname">dscript.fasta.</code><code class="sig-name descname">write</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">nam</span></em>, <em class="sig-param"><span class="n">seq</span></em>, <em class="sig-param"><span class="n">f</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#dscript.fasta.write" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Write a file in <code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
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<li><p><strong>nam</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – List of names</p></li> |
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<li><p><strong>seq</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – List of sequences</p></li> |
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<li><p><strong>f</strong> (<em>_io.TextIOWrapper</em>) – Output file object</p></li> |
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</ul> |
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</dd> |
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</dl> |
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</dd></dl> |
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</div> |
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<div class="section" id="dscript-language-model"> |
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<h2>dscript.language_model<a class="headerlink" href="#dscript-language-model" title="Permalink to this headline">¶</a></h2> |
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</div> |
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<div class="section" id="dscript-pretrained"> |
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<h2>dscript.pretrained<a class="headerlink" href="#dscript-pretrained" title="Permalink to this headline">¶</a></h2> |
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</div> |
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<div class="section" id="dscript-utils"> |
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<h2>dscript.utils<a class="headerlink" href="#dscript-utils" title="Permalink to this headline">¶</a></h2> |
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</div> |
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