Automated update 0b57f76305df926cfb7aaabebc78de8214177a53

dev/api/Bio.SeqIO.FastaIO.html

@@ -479,6 +479,11 @@
 <p>Class to write Fasta format files (OBSOLETE).</p>
 <p>Please use the <code class="docutils literal notranslate"><span class="pre">as_fasta</span></code> function instead, or the top level
 <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO.write()</span></code> function instead using <code class="docutils literal notranslate"><span class="pre">format=&quot;fasta&quot;</span></code>.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaWriter.modes">
+<span class="sig-name descname"><span class="pre">modes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'t'</span></em><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaWriter.modes" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="Bio.SeqIO.FastaIO.FastaWriter.__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">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wrap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">60</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record2title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.FastaIO.FastaWriter.__init__" title="Link to this definition"></a></dt>

dev/api/Bio.SeqIO.InsdcIO.html

@@ -404,7 +404,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.InsdcIO.GenBankWriter">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">GenBankWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'w'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.GenBankWriter" title="Link 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.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">GenBankWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.GenBankWriter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">_InsdcWriter</span></code></p>
 <p>GenBank writer.</p>
 <dl class="py attribute">
@@ -452,7 +452,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.InsdcIO.EmblWriter">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">EmblWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'w'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.EmblWriter" title="Link 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.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">EmblWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.EmblWriter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">_InsdcWriter</span></code></p>
 <p>EMBL writer.</p>
 <dl class="py attribute">
@@ -510,7 +510,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.InsdcIO.ImgtWriter">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">ImgtWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'w'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.ImgtWriter" title="Link 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.InsdcIO.</span></span><span class="sig-name descname"><span class="pre">ImgtWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.InsdcIO.ImgtWriter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="#Bio.SeqIO.InsdcIO.EmblWriter" title="Bio.SeqIO.InsdcIO.EmblWriter"><code class="xref py py-class docutils literal notranslate"><span class="pre">EmblWriter</span></code></a></p>
 <p>IMGT writer (EMBL format variant).</p>
 <dl class="py attribute">

dev/api/Bio.SeqIO.Interfaces.html

@@ -222,7 +222,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.Interfaces.SequenceWriter">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.Interfaces.</span></span><span class="sig-name descname"><span class="pre">SequenceWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'w'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.Interfaces.SequenceWriter" title="Link 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.Interfaces.</span></span><span class="sig-name descname"><span class="pre">SequenceWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.Interfaces.SequenceWriter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Base class for sequence writers. This class should be subclassed.</p>
 <p>It is intended for sequential file formats with an (optional)
@@ -235,9 +235,19 @@
 followed finally by write_footer().</p>
 <p>Note that write_header() cannot require any assumptions about
 the number of records.</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="Bio.SeqIO.Interfaces.SequenceWriter.modes">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">modes</span></span><a class="headerlink" href="#Bio.SeqIO.Interfaces.SequenceWriter.modes" title="Link to this definition"></a></dt>
+<dd><p>File modes (binary or text) that the writer can handle.</p>
+<p>This property must be “t” (for text mode only), “b” (for binary mode
+only), “tb” (if both text and binary mode are accepted, but text mode
+is preferred), or “bt” (if both text and binary mode are accepted, but
+binary mode is preferred).</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="Bio.SeqIO.Interfaces.SequenceWriter.__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">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'w'</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.Interfaces.SequenceWriter.__init__" title="Link 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">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</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.Interfaces.SequenceWriter.__init__" title="Link to this definition"></a></dt>
 <dd><p>Create the writer object.</p>
 </dd></dl>
 

dev/api/Bio.SeqIO.NibIO.html

@@ -232,6 +232,11 @@
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.NibIO.</span></span><span class="sig-name descname"><span class="pre">NibWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.NibIO.NibWriter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="Bio.SeqIO.Interfaces.html#Bio.SeqIO.Interfaces.SequenceWriter" title="Bio.SeqIO.Interfaces.SequenceWriter"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceWriter</span></code></a></p>
 <p>Nib file writer.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="Bio.SeqIO.NibIO.NibWriter.modes">
+<span class="sig-name descname"><span class="pre">modes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'b'</span></em><a class="headerlink" href="#Bio.SeqIO.NibIO.NibWriter.modes" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="Bio.SeqIO.NibIO.NibWriter.__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">target</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.NibIO.NibWriter.__init__" title="Link to this definition"></a></dt>