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<h1>Source code for dscript.fasta</h1><div class="highlight"><pre> |
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<div class="viewcode-block" id="parse"><a class="viewcode-back" href="../../api/index.html#dscript.fasta.parse">[docs]</a><span></span><span class="k">def</span> <span class="nf">parse</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">comment</span><span class="o">=</span><span class="s2">"#"</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Parse a file in ``.fasta`` format.</span> |
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<span class="sd"> :param f: Input file object</span> |
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<span class="sd"> :type f: _io.TextIOWrapper</span> |
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<span class="sd"> :param comment: Character used for comments</span> |
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<span class="sd"> :type comment: str</span> |
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<span class="sd"> :return: names, sequence</span> |
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<span class="sd"> :rtype: list[str], list[str]</span> |
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<span class="sd"> """</span> |
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<span class="n">starter</span> <span class="o">=</span> <span class="s2">">"</span> |
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<span class="n">empty</span> <span class="o">=</span> <span class="s2">""</span> |
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<span class="k">if</span> <span class="s2">"b"</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">mode</span><span class="p">:</span> |
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<span class="n">comment</span> <span class="o">=</span> <span class="sa">b</span><span class="s2">"#"</span> |
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<span class="n">starter</span> <span class="o">=</span> <span class="sa">b</span><span class="s2">">"</span> |
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<span class="n">empty</span> <span class="o">=</span> <span class="sa">b</span><span class="s2">""</span> |
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<span class="n">names</span> <span class="o">=</span> <span class="p">[]</span> |
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<span class="n">sequences</span> <span class="o">=</span> <span class="p">[]</span> |
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<span class="n">name</span> <span class="o">=</span> <span class="kc">None</span> |
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<span class="n">sequence</span> <span class="o">=</span> <span class="p">[]</span> |
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<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span> |
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<span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">comment</span><span class="p">):</span> |
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<span class="k">continue</span> |
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<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> |
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<span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">starter</span><span class="p">):</span> |
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<span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="n">names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> |
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<span class="n">sequences</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">empty</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sequence</span><span class="p">))</span> |
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<span class="n">name</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> |
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<span class="n">sequence</span> <span class="o">=</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">sequence</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span> |
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<span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span> |
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<span class="n">names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> |
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<span class="n">sequences</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">empty</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sequence</span><span class="p">))</span> |
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<span class="k">return</span> <span class="n">names</span><span class="p">,</span> <span class="n">sequences</span></div> |
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<div class="viewcode-block" id="parse_directory"><a class="viewcode-back" href="../../api/index.html#dscript.fasta.parse_directory">[docs]</a><span class="k">def</span> <span class="nf">parse_directory</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span> <span class="n">extension</span><span class="o">=</span><span class="s2">".seq"</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Parse all files in a directory ending with ``extension``.</span> |
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<span class="sd"> :param directory: Input directory</span> |
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<span class="sd"> :type directory: str</span> |
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<span class="sd"> :param extension: Extension of all files to read in</span> |
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<span class="sd"> :type extension: str</span> |
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<span class="sd"> :return: names, sequence</span> |
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<span class="sd"> :rtype: list[str], list[str]</span> |
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<span class="sd"> """</span> |
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<span class="n">names</span> <span class="o">=</span> <span class="p">[]</span> |
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<span class="n">sequences</span> <span class="o">=</span> <span class="p">[]</span> |
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<span class="k">for</span> <span class="n">seqPath</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span> |
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<span class="k">if</span> <span class="n">seqPath</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="n">extension</span><span class="p">):</span> |
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<span class="n">n</span><span class="p">,</span> <span class="n">s</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="sa">f</span><span class="s2">"</span><span class="si">{directory}</span><span class="s2">/</span><span class="si">{seqPath}</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"rb"</span><span class="p">))</span> |
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<span class="n">names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">"utf-8"</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> |
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<span class="n">sequences</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">"utf-8"</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> |
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<span class="k">return</span> <span class="n">names</span><span class="p">,</span> <span class="n">sequences</span></div> |
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<div class="viewcode-block" id="write"><a class="viewcode-back" href="../../api/index.html#dscript.fasta.write">[docs]</a><span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="n">nam</span><span class="p">,</span> <span class="n">seq</span><span class="p">,</span> <span class="n">f</span><span class="p">):</span> |
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<span class="sd">"""</span> |
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<span class="sd"> Write a file in ``.fasta`` format.</span> |
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<span class="sd"> :param nam: List of names</span> |
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<span class="sd"> :type nam: list[str]</span> |
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<span class="sd"> :param seq: List of sequences</span> |
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<span class="sd"> :type seq: list[str]</span> |
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<span class="sd"> :param f: Output file object</span> |
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<span class="sd"> :type f: _io.TextIOWrapper</span> |
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<span class="sd"> """</span> |
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<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">nam</span><span class="p">,</span> <span class="n">seq</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="s2">"></span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">n</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="s2">"</span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">s</span><span class="p">))</span></div> |
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