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<!DOCTYPE html>
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<h1><a href="/index.html">Codon Alignment GSoC Homepage </a></h1>
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<li class="active"><a href="/category/gsoc.html">GSoC</a></li>
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<h1 class="entry-title">
<a href="4th-diary.html" rel="bookmark"
title="Permalink to 4th Diary">4th Diary</a></h1>
</header>
<div class="entry-content">
<footer class="post-info">
<abbr class="published" title="2013-07-22T09:36:00">
Mon 22 July 2013
</abbr>
<address class="vcard author">
By <a class="url fn" href="/author/zheng-ruan.html">Zheng Ruan</a>
</address>
<p>In <a href="/category/gsoc.html">GSoC</a>. </p>
<p>tags: <a href="/tag/codon-alignment.html">Codon Alignment</a><a href="/tag/gsoc.html">GSoC</a></p></footer><!-- /.post-info --> <div class="section" id="things-have-been-done">
<h2>Things have been done</h2>
<p>This week I follows the timeline of my plan and mainly achieves
three things. First I added the backward frameshift support. This
function needs to test in the following weeks and can only handle
a single backward frameshift in an alignment. I need to think about
this more carefully and then write code to allow multiple backward
frameshit events. I don't anticipate the function to be able to deal
with all the situations as it is an inherent difficulty to detect
multiple backward frameshift in one anchor. Next, as my code grows
more than 1000 lines, I reorganize them into different files
(<tt class="docutils literal">CodonSeq.py</tt>, <tt class="docutils literal">CodonAlphabet.py</tt>, <tt class="docutils literal">CodonAlignment.py</tt> and
<tt class="docutils literal">__init__.py</tt>) for
easy management. It also logically easier to use (<tt class="docutils literal">build</tt> method is
in <tt class="docutils literal">__init__.py</tt>). I also added some enhancement in <tt class="docutils literal">CodonSeq</tt>.</p>
<ol class="arabic simple">
<li>Numpy style slice for <tt class="docutils literal">CodonAlignment</tt> is now available;</li>
<li><tt class="docutils literal">CodonSeq</tt> slice will output a <tt class="docutils literal">CodonSeq</tt> if the slice is suitable
for that, otherwise output a <tt class="docutils literal">Seq</tt> object;</li>
<li><tt class="docutils literal">CodonSeq.ungap()</tt> method will return a <tt class="docutils literal">CodonSeq</tt> object.</li>
</ol>
</div>
<div class="section" id="some-examples">
<h2>Some Examples</h2>
<p>As usual, I will write some simple examples to demonstrate the new
features.</p>
<ol class="arabic simple">
<li>Backward frameshift support.</li>
</ol>
<div class="highlight"><pre> <span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.Alphabet</span> <span class="kn">import</span> <span class="n">IUPAC</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.Seq</span> <span class="kn">import</span> <span class="n">Seq</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.SeqRecord</span> <span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.Align</span> <span class="kn">import</span> <span class="n">MultipleSeqAlignment</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.CodonAlign</span> <span class="kn">import</span> <span class="n">build</span>
<span class="o">>>></span> <span class="n">seq1</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">Seq</span><span class="p">(</span><span class="s">'TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG'</span><span class="p">,</span>
<span class="o">...</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">IUPACUnambiguousDNA</span><span class="p">()),</span> <span class="nb">id</span><span class="o">=</span><span class="s">'pro1'</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">seq2</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">Seq</span><span class="p">(</span><span class="s">'TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG'</span><span class="p">,</span>
<span class="o">...</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">IUPACUnambiguousDNA</span><span class="p">()),</span> <span class="nb">id</span><span class="o">=</span><span class="s">'pro2'</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">pro1</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">Seq</span><span class="p">(</span><span class="s">'SGTARTKLLLLLAALCAAGGALE'</span><span class="p">,</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">protein</span><span class="p">),</span> <span class="nb">id</span><span class="o">=</span><span class="s">'pro1'</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">pro2</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">Seq</span><span class="p">(</span><span class="s">'SGTSRTKRLLLLAALGAAGGALE'</span><span class="p">,</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">protein</span><span class="p">),</span> <span class="nb">id</span><span class="o">=</span><span class="s">'pro2'</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">aln</span> <span class="o">=</span> <span class="n">MultipleSeqAlignment</span><span class="p">([</span><span class="n">pro1</span><span class="p">,</span> <span class="n">pro2</span><span class="p">])</span>
<span class="o">>>></span> <span class="n">codon_aln</span> <span class="o">=</span> <span class="n">build</span><span class="p">(</span><span class="n">aln</span><span class="p">,</span> <span class="p">[</span><span class="n">seq1</span><span class="p">,</span> <span class="n">seq2</span><span class="p">])</span>
<span class="o">>>></span> <span class="k">print</span> <span class="n">codon_aln</span>
<span class="n">CodonAlphabet</span><span class="p">()</span> <span class="n">CodonAlignment</span> <span class="k">with</span> <span class="mi">2</span> <span class="n">rows</span> <span class="ow">and</span> <span class="mi">69</span> <span class="n">columns</span> <span class="p">(</span><span class="mi">23</span> <span class="n">codons</span><span class="p">)</span>
<span class="n">TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGT</span><span class="o">...</span><span class="n">GAG</span> <span class="n">pro1</span>
<span class="n">TCAGGGACTTCGAGAACCAAGCG</span><span class="o">-</span><span class="n">CTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGT</span><span class="o">...</span><span class="n">GAG</span> <span class="n">pro2</span>
<span class="c"># 1 2 3 4 5 6 7 8 9</span>
</pre></div>
<p>We can see in the 8th codon of <tt class="docutils literal">pro2</tt>. It is represented as <tt class="docutils literal">CG-</tt>,
meaning there is a backward frameshift events. The 8th codon for <tt class="docutils literal">pro2</tt>
is <tt class="docutils literal">CGC</tt> and the 9th codon is <tt class="docutils literal">CTC</tt>, in which the middle <tt class="docutils literal">C</tt> is
used twice.</p>
<ol class="arabic simple" start="2">
<li>I will then show some examples regarding the new features in
<tt class="docutils literal">CodonSeq.py</tt>.</li>
</ol>
<div class="highlight"><pre><span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio</span> <span class="kn">import</span> <span class="n">SeqIO</span><span class="p">,</span> <span class="n">AlignIO</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">Bio.CodonAlign</span> <span class="kn">import</span> <span class="n">default_codon_alphabet</span>
<span class="o">>>></span> <span class="n">shift_nucl</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="s">'test_data/frame.fa'</span><span class="p">,</span> <span class="s">'fasta'</span><span class="p">,</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">IUPACUnambiguousDNA</span><span class="p">())</span>
<span class="o">>>></span> <span class="n">shift_aln</span> <span class="o">=</span> <span class="n">AlignIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s">'test_data/frame.aln'</span><span class="p">,</span> <span class="s">'clustal'</span><span class="p">,</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">IUPAC</span><span class="o">.</span><span class="n">protein</span><span class="p">)</span>
<span class="o">>>></span> <span class="nb">id</span> <span class="o">=</span> <span class="p">{</span><span class="n">i</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]:</span> <span class="n">i</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s">'test_data/egfr_id'</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">()}</span>
<span class="o">>>></span> <span class="n">shift</span> <span class="o">=</span> <span class="n">build</span><span class="p">(</span><span class="n">shift_aln</span><span class="p">,</span> <span class="n">shift_nucl</span><span class="p">,</span> <span class="n">corr_dict</span><span class="o">=</span><span class="nb">id</span><span class="p">,</span> <span class="n">alphabet</span><span class="o">=</span><span class="n">default_codon_alphabet</span><span class="p">,</span> <span class="n">complete_protein</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
<span class="o">/</span><span class="n">home</span><span class="o">/</span><span class="n">rz</span><span class="o">/</span><span class="n">Working</span><span class="o">.</span><span class="n">Dir</span><span class="o">/</span><span class="n">GSoC</span><span class="o">/</span><span class="n">biopython</span><span class="o">/</span><span class="n">Bio</span><span class="o">/</span><span class="n">CodonAlign</span><span class="o">/</span><span class="n">__init__</span><span class="o">.</span><span class="n">py</span><span class="p">:</span><span class="mi">505</span><span class="p">:</span> <span class="ne">UserWarning</span><span class="p">:</span> <span class="n">gi</span><span class="o">|</span><span class="mi">47522840</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NP_999172</span><span class="o">.</span><span class="mi">1</span><span class="o">|</span> <span class="p">(</span><span class="n">L</span> <span class="mi">449</span><span class="p">)</span> <span class="n">does</span> <span class="ow">not</span> <span class="n">correspond</span> <span class="n">to</span> <span class="n">gi</span><span class="o">|</span><span class="mi">47522839</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_214007</span><span class="o">.</span><span class="mi">1</span><span class="o">|</span> <span class="p">(</span><span class="n">ATG</span><span class="p">)</span>
<span class="o">%</span> <span class="p">(</span><span class="n">pro</span><span class="o">.</span><span class="n">id</span><span class="p">,</span> <span class="n">aa</span><span class="p">,</span> <span class="n">aa_num</span><span class="p">,</span> <span class="n">nucl</span><span class="o">.</span><span class="n">id</span><span class="p">,</span> <span class="n">this_codon</span><span class="p">))</span>
<span class="o">>>></span> <span class="k">print</span> <span class="n">shift</span>
<span class="n">Gapped</span><span class="p">(</span><span class="n">CodonAlphabet</span><span class="p">(),</span> <span class="s">'-'</span><span class="p">)</span> <span class="n">CodonAlignment</span> <span class="k">with</span> <span class="mi">6</span> <span class="n">rows</span> <span class="ow">and</span> <span class="mi">4449</span> <span class="n">columns</span> <span class="p">(</span><span class="mi">1483</span> <span class="n">codons</span><span class="p">)</span>
<span class="n">ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAGCAGCTCC</span><span class="o">...</span><span class="n">GTG</span> <span class="n">gi</span><span class="o">|</span><span class="mi">24657088</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_057410</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="o">---------------------</span><span class="n">ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCCTTC</span><span class="o">...</span><span class="n">GTG</span> <span class="n">gi</span><span class="o">|</span><span class="mi">24657104</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_057411</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="o">------------------------------</span><span class="n">ATGAAAAAGCACGAG</span><span class="o">------------...</span><span class="n">GCC</span> <span class="n">gi</span><span class="o">|</span><span class="mi">302179500</span><span class="o">|</span><span class="n">gb</span><span class="o">|</span><span class="n">HM749883</span><span class="o">.</span><span class="mi">1</span><span class="o">|</span>
<span class="o">------------------------------</span><span class="n">ATGCGACGCTCCTGGGCGGGCGGCGCC</span><span class="o">...</span><span class="n">GCA</span> <span class="n">gi</span><span class="o">|</span><span class="mi">47522839</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_214007</span><span class="o">.</span><span class="mi">1</span><span class="o">|</span>
<span class="o">------------------------------</span><span class="n">ATGCGACCCTCCGGGACGGCCGGGGCA</span><span class="o">...</span><span class="n">GCA</span> <span class="n">gi</span><span class="o">|</span><span class="mi">41327737</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_005228</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="o">------------------------------</span><span class="n">ATGCGACCCTCAGGGACTGCGAGAACC</span><span class="o">...</span><span class="n">GCA</span> <span class="n">gi</span><span class="o">|</span><span class="mi">6478867</span><span class="o">|</span><span class="n">gb</span><span class="o">|</span><span class="n">M37394</span><span class="o">.</span><span class="mi">2</span><span class="o">|</span><span class="n">RATEGFR</span>
<span class="n">Now</span> <span class="n">we</span> <span class="n">have</span> <span class="n">a</span> <span class="n">shift</span> <span class="n">variable</span> <span class="n">storing</span> <span class="n">a</span> <span class="n">CodonAlignment</span> <span class="nb">object</span><span class="o">.</span>
<span class="o">>>></span> <span class="k">print</span> <span class="n">shift</span><span class="p">[:</span><span class="mi">3</span><span class="p">,</span><span class="mi">15</span><span class="p">:</span><span class="mi">51</span><span class="p">]</span>
<span class="n">Gapped</span><span class="p">(</span><span class="n">CodonAlphabet</span><span class="p">(),</span> <span class="s">'-'</span><span class="p">)</span> <span class="n">alignment</span> <span class="k">with</span> <span class="mi">3</span> <span class="n">rows</span> <span class="ow">and</span> <span class="mi">36</span> <span class="n">columns</span>
<span class="n">ATGTGGATGAGCATATCGCGAGGATTGTGGGACAGC</span> <span class="n">gi</span><span class="o">|</span><span class="mi">24657088</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_057410</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="o">------</span><span class="n">ATGCTGCTGCGACGGCGCAACGGCCCCTGC</span> <span class="n">gi</span><span class="o">|</span><span class="mi">24657104</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_057411</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="o">---------------</span><span class="n">ATGAAAAAGCACGAG</span><span class="o">------</span> <span class="n">gi</span><span class="o">|</span><span class="mi">302179500</span><span class="o">|</span><span class="n">gb</span><span class="o">|</span><span class="n">HM749883</span><span class="o">.</span><span class="mi">1</span><span class="o">|</span>
<span class="o">>>></span> <span class="n">rec</span> <span class="o">=</span> <span class="n">shift</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="o">>>></span> <span class="k">print</span> <span class="n">rec</span>
<span class="n">ID</span><span class="p">:</span> <span class="n">gi</span><span class="o">|</span><span class="mi">24657104</span><span class="o">|</span><span class="n">ref</span><span class="o">|</span><span class="n">NM_057411</span><span class="o">.</span><span class="mi">3</span><span class="o">|</span>
<span class="n">Name</span><span class="p">:</span> <span class="o"><</span><span class="n">unknown</span> <span class="n">name</span><span class="o">></span>
<span class="n">Description</span><span class="p">:</span> <span class="o"><</span><span class="n">unknown</span> <span class="n">description</span><span class="o">></span>
<span class="n">Number</span> <span class="n">of</span> <span class="n">features</span><span class="p">:</span> <span class="mi">0</span>
<span class="n">CodonSeq</span><span class="p">(</span><span class="s">'---------------------ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCC...GTG'</span><span class="p">,</span> <span class="n">Gapped</span><span class="p">(</span><span class="n">CodonAlphabet</span><span class="p">(),</span> <span class="s">'-'</span><span class="p">))</span>
<span class="o">>>></span> <span class="k">print</span> <span class="nb">type</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="mi">21</span><span class="p">:</span><span class="mi">39</span><span class="p">])</span>
<span class="o"><</span><span class="k">class</span> <span class="err">'</span><span class="nc">CodonSeq</span><span class="o">.</span><span class="n">CodonSeq</span><span class="s">'></span>
<span class="o">>>></span> <span class="k">print</span> <span class="nb">type</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="mi">21</span><span class="p">:</span><span class="mi">40</span><span class="p">])</span>
<span class="o"><</span><span class="k">class</span> <span class="err">'</span><span class="nc">Bio</span><span class="o">.</span><span class="n">Seq</span><span class="o">.</span><span class="n">Seq</span><span class="s">'></span>
<span class="o">>>></span> <span class="k">print</span> <span class="nb">type</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="o">.</span><span class="n">ungap</span><span class="p">())</span>
<span class="o"><</span><span class="k">class</span> <span class="err">'</span><span class="nc">CodonSeq</span><span class="o">.</span><span class="n">CodonSeq</span><span class="s">'></span>
</pre></div>
<p>It is worth noting here that in-frame slice and <tt class="docutils literal">ungap()</tt> method
retained the <tt class="docutils literal">rf_table</tt> defined in <tt class="docutils literal">CodonSeq</tt>.</p>
</div>
<div class="section" id="future-plan">
<h2>Future Plan</h2>
<ol class="arabic simple">
<li>Allow multiple backward frameshift;</li>
<li>Some support for mixed events (mismatch and frameshift);</li>
<li>Write doctest and mid-term evaluation.</li>
</ol>
<p>For more info, please visit my
[CodonAlign github repo](<a class="reference external" href="https://github.com/zruan/biopython/tree/master/Bio/CodonAlign">https://github.com/zruan/biopython/tree/master/Bio/CodonAlign</a>)</p>
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