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<li>dscript.alphabets</li> |
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<h1>Source code for dscript.alphabets</h1><div class="highlight"><pre> |
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<span></span><span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span> |
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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span> |
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<div class="viewcode-block" id="Alphabet"><a class="viewcode-back" href="../../api/index.html#dscript.alphabets.Alphabet">[docs]</a><span class="k">class</span> <span class="nc">Alphabet</span><span class="p">:</span> |
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<span class="sd">"""</span> |
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<span class="sd"> From `Bepler & Berger <https://github.com/tbepler/protein-sequence-embedding-iclr2019>`_.</span> |
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<span class="sd"> :param chars: List of characters in alphabet</span> |
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<span class="sd"> :type chars: byte str</span> |
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<span class="sd"> :param encoding: Mapping of characters to numbers [default: encoding]</span> |
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<span class="sd"> :type encoding: np.ndarray</span> |
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<span class="sd"> :param mask: Set encoding mask [default: False]</span> |
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<span class="sd"> :type mask: bool</span> |
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<span class="sd"> :param missing: Number to use for a value outside the alphabet [default: 255]</span> |
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<span class="sd"> :type missing: int</span> |
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<span class="sd"> """</span> |
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<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">chars</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">missing</span><span class="o">=</span><span class="mi">255</span><span class="p">):</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">chars</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">frombuffer</span><span class="p">(</span><span class="n">chars</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">encoding</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">256</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span> <span class="o">+</span> <span class="n">missing</span> |
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<span class="k">if</span> <span class="n">encoding</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">encoding</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">))</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">size</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">)</span> |
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<span class="k">else</span><span class="p">:</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">encoding</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">]</span> <span class="o">=</span> <span class="n">encoding</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">size</span> <span class="o">=</span> <span class="n">encoding</span><span class="o">.</span><span class="n">max</span><span class="p">()</span> <span class="o">+</span> <span class="mi">1</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">mask</span> <span class="o">=</span> <span class="n">mask</span> |
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<span class="k">if</span> <span class="n">mask</span><span class="p">:</span> |
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<span class="bp">self</span><span class="o">.</span><span class="n">size</span> <span class="o">-=</span> <span class="mi">1</span> |
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<span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">size</span> |
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<span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span> |
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<span class="k">return</span> <span class="nb">chr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> |
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<div class="viewcode-block" id="Alphabet.encode"><a class="viewcode-back" href="../../api/index.html#dscript.alphabets.Alphabet.encode">[docs]</a> <span class="k">def</span> <span class="nf">encode</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Encode a byte string into alphabet indices</span> |
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<span class="sd"> </span> |
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<span class="sd"> :param x: Amino acid string</span> |
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<span class="sd"> :type x: byte str</span> |
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<span class="sd"> :return: Numeric encoding</span> |
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<span class="sd"> :rtype: np.ndarray</span> |
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<span class="sd"> """</span> |
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<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">frombuffer</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span> |
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">encoding</span><span class="p">[</span><span class="n">x</span><span class="p">]</span></div> |
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<div class="viewcode-block" id="Alphabet.decode"><a class="viewcode-back" href="../../api/index.html#dscript.alphabets.Alphabet.decode">[docs]</a> <span class="k">def</span> <span class="nf">decode</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Decode numeric encoding to byte string of this alphabet</span> |
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<span class="sd"> :param x: Numeric encoding</span> |
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<span class="sd"> :type x: np.ndarray</span> |
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<span class="sd"> :return: Amino acid string</span> |
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<span class="sd"> :rtype: byte str</span> |
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<span class="sd"> """</span> |
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<span class="n">string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chars</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> |
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<span class="k">return</span> <span class="n">string</span><span class="o">.</span><span class="n">tobytes</span><span class="p">()</span></div></div> |
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<div class="viewcode-block" id="Uniprot21"><a class="viewcode-back" href="../../api/index.html#dscript.alphabets.Uniprot21">[docs]</a><span class="k">class</span> <span class="nc">Uniprot21</span><span class="p">(</span><span class="n">Alphabet</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Uniprot 21 Amino Acid Encoding.</span> |
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<span class="sd"> From `Bepler & Berger <https://github.com/tbepler/protein-sequence-embedding-iclr2019>`_.</span> |
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<span class="sd"> """</span> |
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<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> |
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<span class="n">chars</span> <span class="o">=</span> <span class="sa">b</span><span class="s2">"ARNDCQEGHILKMFPSTWYVXOUBZ"</span> |
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<span class="n">encoding</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">chars</span><span class="p">))</span> |
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<span class="n">encoding</span><span class="p">[</span><span class="mi">21</span><span class="p">:]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">11</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">20</span><span class="p">,</span> <span class="mi">20</span><span class="p">]</span> <span class="c1"># encode 'OUBZ' as synonyms</span> |
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<span class="nb">super</span><span class="p">(</span><span class="n">Uniprot21</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">chars</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="n">mask</span><span class="p">,</span> <span class="n">missing</span><span class="o">=</span><span class="mi">20</span><span class="p">)</span></div> |
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© Copyright 2020, Samuel Sledzieski, Rohit Singh |
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