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<h1>Source code for dscript.commands.predict</h1><div class="highlight"><pre> |
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<span></span><span class="sd">"""</span> |
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<span class="sd">Make new predictions with a pre-trained model.</span> |
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<span class="sd">"""</span> |
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<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">os</span> |
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<span class="kn">import</span> <span class="nn">torch</span> |
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<span class="kn">import</span> <span class="nn">h5py</span> |
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<span class="kn">import</span> <span class="nn">argparse</span> |
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<span class="kn">import</span> <span class="nn">datetime</span> |
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<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> |
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<span class="kn">from</span> <span class="nn">scipy.special</span> <span class="kn">import</span> <span class="n">comb</span> |
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<span class="kn">from</span> <span class="nn">tqdm</span> <span class="kn">import</span> <span class="n">tqdm</span> |
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<span class="kn">from</span> <span class="nn">dscript.alphabets</span> <span class="kn">import</span> <span class="n">Uniprot21</span> |
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<span class="kn">from</span> <span class="nn">dscript.fasta</span> <span class="kn">import</span> <span class="n">parse</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">lm_embed</span> |
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<div class="viewcode-block" id="add_args"><a class="viewcode-back" href="../../../api/dscript.commands.html#dscript.commands.predict.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">"--pairs"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Candidate protein pairs to predict"</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">"--model"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Pretrained Model"</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">"--seqs"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Protein sequences in .fasta format"</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">"--embeddings"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"h5 file with embedded sequences"</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">"-o"</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">"File for predictions"</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="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span> |
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<span class="s2">"--thresh"</span><span class="p">,</span> |
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<span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> |
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<span class="n">default</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> |
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<span class="n">help</span><span class="o">=</span><span class="s2">"Positive prediction threshold - used to store contact maps and predictions in a separate file. [default: 0.5]"</span><span class="p">,</span> |
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<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.predict.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 new prediction 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="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">seqs</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">args</span><span class="o">.</span><span class="n">embeddings</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="s2">"One of --seqs or --embeddings is required."</span><span class="p">)</span> |
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<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
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<span class="n">csvPath</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">pairs</span> |
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<span class="n">modelPath</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">model</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">seqPath</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">embPath</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">embeddings</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">threshold</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">thresh</span> |
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<span class="c1"># Set Outpath</span> |
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<span class="k">if</span> <span class="n">outPath</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="n">outPath</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"%Y-%m-</span><span class="si">%d</span><span class="s2">-%H-%M.predictions"</span><span class="p">)</span> |
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<span class="c1"># Set Device</span> |
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<span class="n">use_cuda</span> <span class="o">=</span> <span class="p">(</span><span class="n">device</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">)</span> <span class="ow">and</span> <span class="n">torch</span><span class="o">.</span><span class="n">cuda</span><span class="o">.</span><span class="n">is_available</span><span class="p">()</span> |
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<span class="k">if</span> <span class="n">use_cuda</span><span class="p">:</span> |
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<span class="n">torch</span><span class="o">.</span><span class="n">cuda</span><span class="o">.</span><span class="n">set_device</span><span class="p">(</span><span class="n">device</span><span class="p">)</span> |
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"# Using CUDA device </span><span class="si">{device}</span><span class="s2"> - {torch.cuda.get_device_name(device)}"</span><span class="p">)</span> |
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<span class="k">else</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="s2">"# Using CPU"</span><span class="p">)</span> |
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<span class="c1"># Load Model</span> |
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<span class="k">try</span><span class="p">:</span> |
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<span class="k">if</span> <span class="n">use_cuda</span><span class="p">:</span> |
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<span class="n">model</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">modelPath</span><span class="p">)</span><span class="o">.</span><span class="n">cuda</span><span class="p">()</span> |
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<span class="k">else</span><span class="p">:</span> |
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<span class="n">model</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">modelPath</span><span class="p">)</span><span class="o">.</span><span class="n">cpu</span><span class="p">()</span> |
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<span class="n">model</span><span class="o">.</span><span class="n">use_cuda</span> <span class="o">=</span> <span class="kc">False</span> |
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<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"# Model </span><span class="si">{modelPath}</span><span class="s2"> not found"</span><span class="p">)</span> |
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<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
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<span class="c1"># Load Pairs</span> |
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<span class="k">try</span><span class="p">:</span> |
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<span class="n">pairs</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">csvPath</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> |
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<span class="n">all_prots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">pairs</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">])</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pairs</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]))</span> |
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<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"# Pairs File </span><span class="si">{csvPath}</span><span class="s2"> not found"</span><span class="p">)</span> |
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<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
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<span class="c1"># Load Sequences or Embeddings</span> |
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<span class="k">if</span> <span class="n">embPath</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="k">try</span><span class="p">:</span> |
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<span class="n">names</span><span class="p">,</span> <span class="n">seqs</span> <span class="o">=</span> <span class="n">parse</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">seqPath</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">))</span> |
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<span class="n">seqDict</span> <span class="o">=</span> <span class="p">{</span><span class="n">n</span><span class="p">:</span> <span class="n">s</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span> <span class="n">s</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">names</span><span class="p">,</span> <span class="n">seqs</span><span class="p">)}</span> |
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<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"# Sequence File </span><span class="si">{fastaPath}</span><span class="s2"> not found"</span><span class="p">)</span> |
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<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
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<span class="nb">print</span><span class="p">(</span><span class="s2">"# Generating Embeddings..."</span><span class="p">)</span> |
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<span class="n">embeddings</span> <span class="o">=</span> <span class="p">{}</span> |
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<span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">all_prots</span><span class="p">):</span> |
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<span class="n">embeddings</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">lm_embed</span><span class="p">(</span><span class="n">seqDict</span><span class="p">[</span><span class="n">n</span><span class="p">],</span> <span class="n">use_cuda</span><span class="p">)</span> |
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<span class="k">else</span><span class="p">:</span> |
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<span class="nb">print</span><span class="p">(</span><span class="s2">"# Loading Embeddings..."</span><span class="p">)</span> |
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<span class="n">embedH5</span> <span class="o">=</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">embPath</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> |
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<span class="n">embeddings</span> <span class="o">=</span> <span class="p">{}</span> |
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<span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">all_prots</span><span class="p">):</span> |
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<span class="n">embeddings</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">from_numpy</span><span class="p">(</span><span class="n">embedH5</span><span class="p">[</span><span class="n">n</span><span class="p">][:])</span> |
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<span class="n">embedH5</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
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<span class="c1"># Make Predictions</span> |
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<span class="nb">print</span><span class="p">(</span><span class="s2">"# Making Predictions..."</span><span class="p">)</span> |
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<span class="n">n</span> <span class="o">=</span> <span class="mi">0</span> |
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<span class="n">outPathAll</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{outPath}</span><span class="s2">.tsv"</span> |
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<span class="n">outPathPos</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{outPath}</span><span class="s2">.positive.tsv"</span> |
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<span class="n">cmap_file</span> <span class="o">=</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{outPath}</span><span class="s2">.cmaps.h5"</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> |
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<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outPathAll</span><span class="p">,</span> <span class="s2">"w+"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> |
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<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outPathPos</span><span class="p">,</span> <span class="s2">"w+"</span><span class="p">)</span> <span class="k">as</span> <span class="n">pos_f</span><span class="p">:</span> |
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<span class="k">with</span> <span class="n">torch</span><span class="o">.</span><span class="n">no_grad</span><span class="p">():</span> |
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<span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="p">(</span><span class="n">n0</span><span class="p">,</span> <span class="n">n1</span><span class="p">)</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">pairs</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">iterrows</span><span class="p">(),</span> <span class="n">total</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">pairs</span><span class="p">)):</span> |
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<span class="n">n0</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">n0</span><span class="p">)</span> |
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<span class="n">n1</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">n1</span><span class="p">)</span> |
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<span class="k">if</span> <span class="n">n</span> <span class="o">%</span> <span class="mi">50</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
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<span class="n">f</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span> |
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<span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span> |
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<span class="n">p0</span> <span class="o">=</span> <span class="n">embeddings</span><span class="p">[</span><span class="n">n0</span><span class="p">]</span> |
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<span class="n">p1</span> <span class="o">=</span> <span class="n">embeddings</span><span class="p">[</span><span class="n">n1</span><span class="p">]</span> |
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<span class="k">if</span> <span class="n">use_cuda</span><span class="p">:</span> |
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<span class="n">p0</span> <span class="o">=</span> <span class="n">p0</span><span class="o">.</span><span class="n">cuda</span><span class="p">()</span> |
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<span class="n">p1</span> <span class="o">=</span> <span class="n">p1</span><span class="o">.</span><span class="n">cuda</span><span class="p">()</span> |
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<span class="n">cm</span><span class="p">,</span> <span class="n">p</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">map_predict</span><span class="p">(</span><span class="n">p0</span><span class="p">,</span> <span class="n">p1</span><span class="p">)</span> |
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<span class="n">p</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">item</span><span class="p">()</span> |
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<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{n0}</span><span class="se">\t</span><span class="si">{n1}</span><span class="se">\t</span><span class="si">{p}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> |
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<span class="k">if</span> <span class="n">p</span> <span class="o">>=</span> <span class="n">threshold</span><span class="p">:</span> |
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<span class="n">pos_f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{n0}</span><span class="se">\t</span><span class="si">{n1}</span><span class="se">\t</span><span class="si">{p}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> |
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<span class="n">cmap_file</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{n0}</span><span class="s2">x</span><span class="si">{n1}</span><span class="s2">"</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">cm</span><span class="o">.</span><span class="n">squeeze</span><span class="p">()</span><span class="o">.</span><span class="n">cpu</span><span class="p">()</span><span class="o">.</span><span class="n">numpy</span><span class="p">())</span> |
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<span class="n">cmap_file</span><span class="o">.</span><span class="n">close</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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<p> |
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