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<h1>Source code for dscript.commands.embed</h1><div class="highlight"><pre> |
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<span></span><span class="sd">"""</span> |
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<span class="sd">Generate new embeddings using pre-trained language model.</span> |
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<span class="sd">"""</span> |
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<span class="kn">import</span> <span class="nn">argparse</span> |
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<span class="kn">from</span> <span class="nn">dscript.language_model</span> <span class="kn">import</span> <span class="n">embed_from_fasta</span> |
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<div class="viewcode-block" id="add_args"><a class="viewcode-back" href="../../../api/dscript.commands.html#dscript.commands.embed.add_args">[docs]</a><span class="k">def</span> <span class="nf">add_args</span><span class="p">(</span><span class="n">parser</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Create parser for command line utility.</span> |
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<span class="sd"> :meta private:</span> |
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<span class="sd"> """</span> |
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<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--seqs"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Sequences to be embedded"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> |
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<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--outfile"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"h5 file to write results"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> |
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<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-d"</span><span class="p">,</span> <span class="s2">"--device"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Compute device to use"</span><span class="p">)</span> |
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<span class="k">return</span> <span class="n">parser</span></div> |
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<div class="viewcode-block" id="main"><a class="viewcode-back" href="../../../api/dscript.commands.html#dscript.commands.embed.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">args</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Run embedding from arguments.</span> |
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<span class="sd"> :meta private:</span> |
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<span class="sd"> """</span> |
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<span class="n">inPath</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">seqs</span> |
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<span class="n">outPath</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">outfile</span> |
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<span class="n">device</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">device</span> |
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<span class="n">embed_from_fasta</span><span class="p">(</span><span class="n">inPath</span><span class="p">,</span> <span class="n">outPath</span><span class="p">,</span> <span class="n">device</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div> |
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<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> |
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<span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">)</span> |
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<span class="n">add_args</span><span class="p">(</span><span class="n">parser</span><span class="p">)</span> |
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<span class="n">main</span><span class="p">(</span><span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">())</span> |
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</pre></div> |
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