Automated update 2f86d90c864b282a8ee8d40f95cf9e03097c7e57

dev/api/Bio.SeqIO.FastaIO.html

@@ -199,22 +199,17 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaIterator">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.FastaIO.</span></span><span class="sig-name descname"><span class="pre">FastaIterator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">os.PathLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title2ids</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">Callable</span><span class="p"><span class="pre">[</span></span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaIterator" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.FastaIO.</span></span><span class="sig-name descname"><span class="pre">FastaIterator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">os.PathLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaIterator" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="Bio.SeqIO.Interfaces.html#Bio.SeqIO.Interfaces.SequenceIterator" title="Bio.SeqIO.Interfaces.SequenceIterator"><code class="xref py py-class docutils literal notranslate"><span class="pre">Bio.SeqIO.Interfaces.SequenceIterator</span></code></a></p>
 <p>Parser for Fasta files.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaIterator.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">os.PathLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title2ids</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">Callable</span><span class="p"><span class="pre">[</span></span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaIterator.__init__" title="Permalink to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">os.PathLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaIterator.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Iterate over Fasta records as SeqRecord objects.</p>
 <dl class="simple">
 <dt>Arguments:</dt><dd><ul class="simple">
 <li><p>source - input stream opened in text mode, or a path to a file</p></li>
 <li><p>alphabet - optional alphabet, not used. Leave as None.</p></li>
-<li><p>title2ids (DEPRECATED) - A function that, when given the title of
-the FASTA file (without the beginning &gt;), will return the id, name
-and description (in that order) for the record as a tuple of strings.
-If this is not given, then the entire title line will be used
-as the description, and the first word as the id and name.</p></li>
 </ul>
 </dd>
 </dl>
@@ -231,22 +226,8 @@
 <span class="go">delta</span>
 </pre></div>
 </div>
-<p>However, you can supply a title2ids function to alter this (DEPRECATED):</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="k">def</span> <span class="nf">take_upper</span><span class="p">(</span><span class="n">title</span><span class="p">):</span>
-<span class="gp">... </span>    <span class="k">return</span> <span class="n">title</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span> <span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">title</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;Fasta/dups.fasta&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">handle</span><span class="p">:</span>
-<span class="gp">... </span>    <span class="k">for</span> <span class="n">record</span> <span class="ow">in</span> <span class="n">FastaIterator</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span> <span class="n">title2ids</span><span class="o">=</span><span class="n">take_upper</span><span class="p">):</span>
-<span class="gp">... </span>        <span class="nb">print</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
-<span class="gp">...</span>
-<span class="go">ALPHA</span>
-<span class="go">BETA</span>
-<span class="go">GAMMA</span>
-<span class="go">ALPHA</span>
-<span class="go">DELTA</span>
-</pre></div>
-</div>
-<p>Instead of title2ids, please use a generator function to modify the
-records:</p>
+<p>If you want to modify the records before writing, for example to change
+the ID of each record, you can use a generator function as follows:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="k">def</span> <span class="nf">modify_records</span><span class="p">(</span><span class="n">records</span><span class="p">):</span>
 <span class="gp">... </span>    <span class="k">for</span> <span class="n">record</span> <span class="ow">in</span> <span class="n">records</span><span class="p">:</span>
 <span class="gp">... </span>        <span class="n">record</span><span class="o">.</span><span class="n">id</span> <span class="o">=</span> <span class="n">record</span><span class="o">.</span><span class="n">id</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>