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155 changes: 154 additions & 1 deletion dev/api/Bio.SeqIO.FastaIO.html
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16 changes: 16 additions & 0 deletions dev/api/Bio.SeqIO.html
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Expand Up @@ -171,6 +171,22 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__init__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.parse"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.parse()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.iterate"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.iterate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__abstractmethods__</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator.__parameters__</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaWriter"><code class="docutils literal notranslate"><span class="pre">FastaWriter</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaWriter.__init__"><code class="docutils literal notranslate"><span class="pre">FastaWriter.__init__()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaWriter.write_record"><code class="docutils literal notranslate"><span class="pre">FastaWriter.write_record()</span></code></a></li>
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2 changes: 2 additions & 0 deletions dev/api/Bio.html
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Expand Up @@ -1731,6 +1731,8 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineParser"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineParser()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator"><code class="docutils literal notranslate"><span class="pre">FastaIterator</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineIterator</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator"><code class="docutils literal notranslate"><span class="pre">FastaBlastIterator</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator"><code class="docutils literal notranslate"><span class="pre">FastaPearsonIterator</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaWriter"><code class="docutils literal notranslate"><span class="pre">FastaWriter</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineWriter"><code class="docutils literal notranslate"><span class="pre">FastaTwoLineWriter</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.as_fasta"><code class="docutils literal notranslate"><span class="pre">as_fasta()</span></code></a></li>
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34 changes: 29 additions & 5 deletions dev/genindex.html
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Expand Up @@ -261,8 +261,12 @@ <h2 id="_">_</h2>
<li><a href="api/Bio.SeqFeature.html#Bio.SeqFeature.WithinPosition.__abstractmethods__">(Bio.SeqFeature.WithinPosition attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.AbiIO.html#Bio.SeqIO.AbiIO.AbiIterator.__abstractmethods__">(Bio.SeqIO.AbiIO.AbiIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__abstractmethods__">(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__abstractmethods__">(Bio.SeqIO.FastaIO.FastaIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__abstractmethods__">(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__abstractmethods__">(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)</a>
</li>
Expand Down Expand Up @@ -1489,8 +1493,12 @@ <h2 id="_">_</h2>
<li><a href="api/Bio.SeqFeature.html#Bio.SeqFeature.SimpleLocation.__init__">(Bio.SeqFeature.SimpleLocation method)</a>
</li>
<li><a href="api/Bio.SeqIO.AbiIO.html#Bio.SeqIO.AbiIO.AbiIterator.__init__">(Bio.SeqIO.AbiIO.AbiIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__init__">(Bio.SeqIO.FastaIO.FastaBlastIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__init__">(Bio.SeqIO.FastaIO.FastaIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__init__">(Bio.SeqIO.FastaIO.FastaPearsonIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__init__">(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)</a>
</li>
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<li><a href="api/Bio.PDB.Structure.html#Bio.PDB.Structure.Structure.__parameters__">(Bio.PDB.Structure.Structure attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.AbiIO.html#Bio.SeqIO.AbiIO.AbiIterator.__parameters__">(Bio.SeqIO.AbiIO.AbiIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.__parameters__">(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.__parameters__">(Bio.SeqIO.FastaIO.FastaIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.__parameters__">(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.__parameters__">(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)</a>
</li>
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</li>
</ul></li>
<li><a href="api/Bio.Align.Applications.html#Bio.Align.Applications.MuscleCommandline.fasta">fasta (Bio.Align.Applications.MuscleCommandline property)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator">FastaBlastIterator (class in Bio.SeqIO.FastaIO)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator">FastaIterator (class in Bio.SeqIO.FastaIO)</a>
</li>
Expand All @@ -6807,6 +6821,8 @@ <h2 id="F">F</h2>
<li><a href="api/Bio.Align.Applications.html#Bio.Align.Applications.MafftCommandline.fastapair">fastapair (Bio.Align.Applications.MafftCommandline property)</a>
</li>
<li><a href="api/Bio.Align.Applications.html#Bio.Align.Applications.MafftCommandline.fastaparttree">fastaparttree (Bio.Align.Applications.MafftCommandline property)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator">FastaPearsonIterator (class in Bio.SeqIO.FastaIO)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator">FastaTwoLineIterator (class in Bio.SeqIO.FastaIO)</a>
</li>
Expand Down Expand Up @@ -7012,14 +7028,14 @@ <h2 id="F">F</h2>
</li>
<li><a href="api/Bio.MarkovModel.html#Bio.MarkovModel.find_states">find_states() (in module Bio.MarkovModel)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.phenotype.phen_micro.html#Bio.phenotype.phen_micro.WellRecord.fit">fit() (Bio.phenotype.phen_micro.WellRecord method)</a>

<ul>
<li><a href="api/Bio.phenotype.pm_fitting.html#Bio.phenotype.pm_fitting.fit">(in module Bio.phenotype.pm_fitting)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.Align.Applications.html#Bio.Align.Applications.PrankCommandline.fixedbranches">fixedbranches (Bio.Align.Applications.PrankCommandline property)</a>
</li>
<li><a href="api/Bio.PDB.Atom.html#Bio.PDB.Atom.Atom.flag_disorder">flag_disorder() (Bio.PDB.Atom.Atom method)</a>
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<li><a href="api/Bio.Sequencing.Applications.html#Bio.Sequencing.Applications.SamtoolsIndexCommandline.input_bam">(Bio.Sequencing.Applications.SamtoolsIndexCommandline property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.Blast.Applications.html#Bio.Blast.Applications.NcbimakeblastdbCommandline.input_file">input_file (Bio.Blast.Applications.NcbimakeblastdbCommandline property)</a>

<ul>
Expand All @@ -8466,6 +8480,8 @@ <h2 id="I">I</h2>
<li><a href="api/Bio.Sequencing.Applications.html#Bio.Sequencing.Applications.SamtoolsViewCommandline.input_file">(Bio.Sequencing.Applications.SamtoolsViewCommandline property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/Bio.Phylo.Applications.html#Bio.Phylo.Applications.PhymlCommandline.input_tree">input_tree (Bio.Phylo.Applications.PhymlCommandline property)</a>
</li>
<li><a href="api/Bio.Blast.Applications.html#Bio.Blast.Applications.NcbimakeblastdbCommandline.input_type">input_type (Bio.Blast.Applications.NcbimakeblastdbCommandline property)</a>
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<li><a href="api/BioSQL.BioSeqDatabase.html#BioSQL.BioSeqDatabase.DBServer.items">(BioSQL.BioSeqDatabase.DBServer method)</a>
</li>
</ul></li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.iterate">iterate() (Bio.SeqIO.FastaIO.FastaIterator method)</a>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.iterate">iterate() (Bio.SeqIO.FastaIO.FastaBlastIterator method)</a>

<ul>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.iterate">(Bio.SeqIO.FastaIO.FastaIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.iterate">(Bio.SeqIO.FastaIO.FastaPearsonIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.iterate">(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)</a>
</li>
</ul></li>
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<li><a href="api/Bio.Phylo.PhyloXMLIO.html#Bio.Phylo.PhyloXMLIO.Parser.parse">(Bio.Phylo.PhyloXMLIO.Parser method)</a>
</li>
<li><a href="api/Bio.SeqIO.AbiIO.html#Bio.SeqIO.AbiIO.AbiIterator.parse">(Bio.SeqIO.AbiIO.AbiIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaBlastIterator.parse">(Bio.SeqIO.FastaIO.FastaBlastIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaIterator.parse">(Bio.SeqIO.FastaIO.FastaIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaPearsonIterator.parse">(Bio.SeqIO.FastaIO.FastaPearsonIterator method)</a>
</li>
<li><a href="api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineIterator.parse">(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)</a>
</li>
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2 changes: 1 addition & 1 deletion dev/searchindex.js
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