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<li class="toctree-l1 current"><a class="reference internal" href="index.html">Biopython Tutorial & Cookbook</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="chapter_introduction.html">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_quick_start.html">Quick Start – What can you do with Biopython?</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_seq_objects.html">Sequence objects</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Sequence annotation objects</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#the-seqrecord-object">The SeqRecord object</a></li>
<li class="toctree-l3"><a class="reference internal" href="#creating-a-seqrecord">Creating a SeqRecord</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#seqrecord-objects-from-scratch">SeqRecord objects from scratch</a></li>
<li class="toctree-l4"><a class="reference internal" href="#seqrecord-objects-from-fasta-files">SeqRecord objects from FASTA files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#seqrecord-objects-from-genbank-files">SeqRecord objects from GenBank files</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#feature-location-and-position-objects">Feature, location and position objects</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#seqfeature-objects">SeqFeature objects</a></li>
<li class="toctree-l4"><a class="reference internal" href="#positions-and-locations">Positions and locations</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sequence-described-by-a-feature-or-location">Sequence described by a feature or location</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#comparison">Comparison</a></li>
<li class="toctree-l3"><a class="reference internal" href="#references">References</a></li>
<li class="toctree-l3"><a class="reference internal" href="#the-format-method">The format method</a></li>
<li class="toctree-l3"><a class="reference internal" href="#slicing-a-seqrecord">Slicing a SeqRecord</a></li>
<li class="toctree-l3"><a class="reference internal" href="#adding-seqrecord-objects">Adding SeqRecord objects</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reverse-complementing-seqrecord-objects">Reverse-complementing SeqRecord objects</a></li>
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<li class="toctree-l2"><a class="reference internal" href="chapter_seqio.html">Sequence Input/Output</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_align.html">Sequence alignments</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_pairwise.html">Pairwise sequence alignment</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_msa.html">Multiple Sequence Alignment objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_pairwise2.html">Pairwise alignments using pairwise2</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_blast.html">BLAST (new)</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_blast.html#blast-old">BLAST (old)</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_searchio.html">BLAST and other sequence search tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_entrez.html">Accessing NCBI’s Entrez databases</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_uniprot.html">Swiss-Prot and ExPASy</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_pdb.html">Going 3D: The PDB module</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_popgen.html">Bio.PopGen: Population genetics</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_phylo.html">Phylogenetics with Bio.Phylo</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_motifs.html">Sequence motif analysis using Bio.motifs</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_cluster.html">Cluster analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_graphics.html">Graphics including GenomeDiagram</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter_kegg.html">KEGG</a></li>
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<section id="sequence-annotation-objects">
<span id="chapter-seq-annot"></span><h1>Sequence annotation objects<a class="headerlink" href="#sequence-annotation-objects" title="Link to this heading"></a></h1>
<p>Chapter <a class="reference internal" href="chapter_seq_objects.html#chapter-seq-objects"><span class="std std-ref">Sequence objects</span></a> introduced the
sequence classes. Immediately “above” the <code class="docutils literal notranslate"><span class="pre">Seq</span></code> class is the Sequence
Record or <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> class, defined in the <code class="docutils literal notranslate"><span class="pre">Bio.SeqRecord</span></code> module.
This class allows higher level features such as identifiers and features
(as <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> objects) to be associated with the sequence, and is
used throughout the sequence input/output interface <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code>
described fully in Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a>.</p>
<p>If you are only going to be working with simple data like FASTA files,
you can probably skip this chapter for now. If on the other hand you are
going to be using richly annotated sequence data, say from GenBank or
EMBL files, this information is quite important.</p>
<p>While this chapter should cover most things to do with the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>
and <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> objects in this chapter, you may also want to read
the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> wiki page (<a class="reference external" href="http://biopython.org/wiki/SeqRecord">http://biopython.org/wiki/SeqRecord</a>), and
the built-in documentation (<a class="reference internal" href="../api/Bio.SeqRecord.html#module-Bio.SeqRecord" title="Bio.SeqRecord"><code class="xref py py-mod docutils literal notranslate"><span class="pre">Bio.SeqRecord</span></code></a> and
<a class="reference internal" href="../api/Bio.SeqFeature.html#module-Bio.SeqFeature" title="Bio.SeqFeature"><code class="xref py py-mod docutils literal notranslate"><span class="pre">Bio.SeqFeature</span></code></a>):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqRecord</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="gp">>>> </span><span class="n">help</span><span class="p">(</span><span class="n">SeqRecord</span><span class="p">)</span>
</pre></div>
</div>
<section id="the-seqrecord-object">
<span id="sec-seqrecord"></span><h2>The SeqRecord object<a class="headerlink" href="#the-seqrecord-object" title="Link to this heading"></a></h2>
<p>The <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> (Sequence Record) class is defined in the
<code class="docutils literal notranslate"><span class="pre">Bio.SeqRecord</span></code> module. This class allows higher level features such
as identifiers and features to be associated with a sequence (see
Chapter <a class="reference internal" href="chapter_seq_objects.html#chapter-seq-objects"><span class="std std-ref">Sequence objects</span></a>), and is the
basic data type for the <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code> sequence input/output interface
(see Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a>).</p>
<p>The <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> class itself is quite simple, and offers the following
information as attributes:</p>
<dl class="simple">
<dt>.seq</dt><dd><p>The sequence itself, typically a <code class="docutils literal notranslate"><span class="pre">Seq</span></code> object.</p>
</dd>
<dt>.id</dt><dd><p>The primary ID used to identify the sequence – a string. In most
cases this is something like an accession number.</p>
</dd>
<dt>.name</dt><dd><p>A “common” name/id for the sequence – a string. In some cases this
will be the same as the accession number, but it could also be a
clone name. I think of this as being analogous to the LOCUS id in a
GenBank record.</p>
</dd>
<dt>.description</dt><dd><p>A human readable description or expressive name for the sequence –
a string.</p>
</dd>
<dt>.letter_annotations</dt><dd><p>Holds per-letter-annotations using a (restricted) dictionary of
additional information about the letters in the sequence. The keys
are the name of the information, and the information is contained in
the value as a Python sequence (i.e. a list, tuple or string) with
the same length as the sequence itself. This is often used for
quality scores (e.g.
Section <a class="reference internal" href="chapter_cookbook.html#sec-fastq-filtering-example"><span class="std std-ref">Simple quality filtering for FASTQ files</span></a>)
or secondary structure information (e.g. from Stockholm/PFAM
alignment files).</p>
</dd>
<dt>.annotations</dt><dd><p>A dictionary of additional information about the sequence. The keys
are the name of the information, and the information is contained in
the value. This allows the addition of more “unstructured”
information to the sequence.</p>
</dd>
<dt>.features</dt><dd><p>A list of <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> objects with more structured information
about the features on a sequence (e.g. position of genes on a genome,
or domains on a protein sequence). The structure of sequence features
is described below in Section <a class="reference internal" href="#sec-seq-features"><span class="std std-ref">Feature, location and position objects</span></a>.</p>
</dd>
<dt>.dbxrefs</dt><dd><p>A list of database cross-references as strings.</p>
</dd>
</dl>
</section>
<section id="creating-a-seqrecord">
<h2>Creating a SeqRecord<a class="headerlink" href="#creating-a-seqrecord" title="Link to this heading"></a></h2>
<p>Using a <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> object is not very complicated, since all of the
information is presented as attributes of the class. Usually you won’t
create a <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> “by hand”, but instead use <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code> to read
in a sequence file for you (see
Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a> and the examples below).
However, creating <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> can be quite simple.</p>
<section id="seqrecord-objects-from-scratch">
<h3>SeqRecord objects from scratch<a class="headerlink" href="#seqrecord-objects-from-scratch" title="Link to this heading"></a></h3>
<p>To create a <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> at a minimum you just need a <code class="docutils literal notranslate"><span class="pre">Seq</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="n">simple_seq</span> <span class="o">=</span> <span class="n">Seq</span><span class="p">(</span><span class="s2">"GATC"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqRecord</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="gp">>>> </span><span class="n">simple_seq_r</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">simple_seq</span><span class="p">)</span>
</pre></div>
</div>
<p>Additionally, you can also pass the id, name and description to the
initialization function, but if not they will be set as strings
indicating they are unknown, and can be modified subsequently:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">id</span>
<span class="go">'<unknown id>'</span>
<span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">id</span> <span class="o">=</span> <span class="s2">"AC12345"</span>
<span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s2">"Made up sequence I wish I could write a paper about"</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">description</span><span class="p">)</span>
<span class="go">Made up sequence I wish I could write a paper about</span>
<span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">seq</span>
<span class="go">Seq('GATC')</span>
</pre></div>
</div>
<p>Including an identifier is very important if you want to output your
<code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> to a file. You would normally include this when creating
the object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="n">simple_seq</span> <span class="o">=</span> <span class="n">Seq</span><span class="p">(</span><span class="s2">"GATC"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqRecord</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="gp">>>> </span><span class="n">simple_seq_r</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span><span class="n">simple_seq</span><span class="p">,</span> <span class="nb">id</span><span class="o">=</span><span class="s2">"AC12345"</span><span class="p">)</span>
</pre></div>
</div>
<p>As mentioned above, the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> has an dictionary attribute
<code class="docutils literal notranslate"><span class="pre">annotations</span></code>. This is used for any miscellaneous annotations that
doesn’t fit under one of the other more specific attributes. Adding
annotations is easy, and just involves dealing directly with the
annotation dictionary:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="s2">"evidence"</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"None. I just made it up."</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">annotations</span><span class="p">)</span>
<span class="go">{'evidence': 'None. I just made it up.'}</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="s2">"evidence"</span><span class="p">])</span>
<span class="go">None. I just made it up.</span>
</pre></div>
</div>
<p>Working with per-letter-annotations is similar, <code class="docutils literal notranslate"><span class="pre">letter_annotations</span></code>
is a dictionary like attribute which will let you assign any Python
sequence (i.e. a string, list or tuple) which has the same length as the
sequence:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">40</span><span class="p">,</span> <span class="mi">40</span><span class="p">,</span> <span class="mi">38</span><span class="p">,</span> <span class="mi">30</span><span class="p">]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">)</span>
<span class="go">{'phred_quality': [40, 40, 38, 30]}</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">simple_seq_r</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">])</span>
<span class="go">[40, 40, 38, 30]</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">dbxrefs</span></code> and <code class="docutils literal notranslate"><span class="pre">features</span></code> attributes are just Python lists, and
should be used to store strings and <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> objects (discussed
later in this chapter) respectively.</p>
</section>
<section id="seqrecord-objects-from-fasta-files">
<h3>SeqRecord objects from FASTA files<a class="headerlink" href="#seqrecord-objects-from-fasta-files" title="Link to this heading"></a></h3>
<p>This example uses a fairly large FASTA file containing the whole
sequence for <em>Yersinia pestis biovar Microtus</em> str. 91001 plasmid pPCP1,
originally downloaded from the NCBI. This file is included with the
Biopython unit tests under the GenBank folder, or online
<a class="reference external" href="https://raw.githubusercontent.com/biopython/biopython/master/Tests/GenBank/NC_005816.fna">NC_005816.fna</a>
from our website.</p>
<p>The file starts like this - and you can check there is only one record
present (i.e. only one line starting with a greater than symbol):</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>>gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus ... pPCP1, complete sequence
TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGGGGGTAATCTGCTCTCC
...
</pre></div>
</div>
<p>Back in Chapter <a class="reference internal" href="chapter_quick_start.html#chapter-quick-start"><span class="std std-ref">Quick Start – What can you do with Biopython?</span></a> you
will have seen the function <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO.parse(...)</span></code> used to loop over
all the records in a file as <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> objects. The <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code>
module has a sister function for use on files which contain just one
record which we’ll use here (see
Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a> for details):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">"NC_005816.fna"</span><span class="p">,</span> <span class="s2">"fasta"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">record</span>
<span class="go">SeqRecord(seq=Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG'), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|', description='gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=[])</span>
</pre></div>
</div>
<p>Now, let’s have a look at the key attributes of this <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>
individually – starting with the <code class="docutils literal notranslate"><span class="pre">seq</span></code> attribute which gives you a
<code class="docutils literal notranslate"><span class="pre">Seq</span></code> object:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">seq</span>
<span class="go">Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG')</span>
</pre></div>
</div>
<p>Next, the identifiers and description:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">id</span>
<span class="go">'gi|45478711|ref|NC_005816.1|'</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">name</span>
<span class="go">'gi|45478711|ref|NC_005816.1|'</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">description</span>
<span class="go">'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence'</span>
</pre></div>
</div>
<p>As you can see above, the first word of the FASTA record’s title line
(after removing the greater than symbol) is used for both the <code class="docutils literal notranslate"><span class="pre">id</span></code> and
<code class="docutils literal notranslate"><span class="pre">name</span></code> attributes. The whole title line (after removing the greater
than symbol) is used for the record description. This is deliberate,
partly for backwards compatibility reasons, but it also makes sense if
you have a FASTA file like this:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>>Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1
TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGGGGGTAATCTGCTCTCC
...
</pre></div>
</div>
<p>Note that none of the other annotation attributes get populated when
reading a FASTA file:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">dbxrefs</span>
<span class="go">[]</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">annotations</span>
<span class="go">{}</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">letter_annotations</span>
<span class="go">{}</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">features</span>
<span class="go">[]</span>
</pre></div>
</div>
<p>In this case our example FASTA file was from the NCBI, and they have a
fairly well defined set of conventions for formatting their FASTA lines.
This means it would be possible to parse this information and extract
the GI number and accession for example. However, FASTA files from other
sources vary, so this isn’t possible in general.</p>
</section>
<section id="seqrecord-objects-from-genbank-files">
<h3>SeqRecord objects from GenBank files<a class="headerlink" href="#seqrecord-objects-from-genbank-files" title="Link to this heading"></a></h3>
<p>As in the previous example, we’re going to look at the whole sequence
for <em>Yersinia pestis biovar Microtus</em> str. 91001 plasmid pPCP1,
originally downloaded from the NCBI, but this time as a GenBank file.
Again, this file is included with the Biopython unit tests under the
GenBank folder, or online
<a class="reference external" href="https://raw.githubusercontent.com/biopython/biopython/master/Tests/GenBank/NC_005816.gb">NC_005816.gb</a>
from our website.</p>
<p>This file contains a single record (i.e. only one LOCUS line) and
starts:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>LOCUS NC_005816 9609 bp DNA circular BCT 21-JUL-2008
DEFINITION Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete
sequence.
ACCESSION NC_005816
VERSION NC_005816.1 GI:45478711
PROJECT GenomeProject:10638
...
</pre></div>
</div>
<p>Again, we’ll use <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code> to read this file in, and the code is
almost identical to that for used above for the FASTA file (see
Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a> for details):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">"NC_005816.gb"</span><span class="p">,</span> <span class="s2">"genbank"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">record</span>
<span class="go">SeqRecord(seq=Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG'), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=['Project:58037'])</span>
</pre></div>
</div>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">seq</span>
<span class="go">Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG')</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">name</span></code> comes from the LOCUS line, while the <code class="docutils literal notranslate"><span class="pre">id</span></code> includes the
version suffix. The description comes from the DEFINITION line:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">id</span>
<span class="go">'NC_005816.1'</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">name</span>
<span class="go">'NC_005816'</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">description</span>
<span class="go">'Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence'</span>
</pre></div>
</div>
<p>GenBank files don’t have any per-letter annotations:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">letter_annotations</span>
<span class="go">{}</span>
</pre></div>
</div>
<p>Most of the annotations information gets recorded in the <code class="docutils literal notranslate"><span class="pre">annotations</span></code>
dictionary, for example:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">annotations</span><span class="p">)</span>
<span class="go">13</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="s2">"source"</span><span class="p">]</span>
<span class="go">'Yersinia pestis biovar Microtus str. 91001'</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">dbxrefs</span></code> list gets populated from any PROJECT or DBLINK lines:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">dbxrefs</span>
<span class="go">['Project:58037']</span>
</pre></div>
</div>
<p>Finally, and perhaps most interestingly, all the entries in the features
table (e.g. the genes or CDS features) get recorded as <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code>
objects in the <code class="docutils literal notranslate"><span class="pre">features</span></code> list.</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">features</span><span class="p">)</span>
<span class="go">41</span>
</pre></div>
</div>
<p>We’ll talk about <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> objects next, in
Section <a class="reference internal" href="#sec-seq-features"><span class="std std-ref">Feature, location and position objects</span></a>.</p>
</section>
</section>
<section id="feature-location-and-position-objects">
<span id="sec-seq-features"></span><h2>Feature, location and position objects<a class="headerlink" href="#feature-location-and-position-objects" title="Link to this heading"></a></h2>
<section id="seqfeature-objects">
<h3>SeqFeature objects<a class="headerlink" href="#seqfeature-objects" title="Link to this heading"></a></h3>
<p>Sequence features are an essential part of describing a sequence. Once
you get beyond the sequence itself, you need some way to organize and
easily get at the more “abstract” information that is known about the
sequence. While it is probably impossible to develop a general sequence
feature class that will cover everything, the Biopython <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code>
class attempts to encapsulate as much of the information about the
sequence as possible. The design is heavily based on the GenBank/EMBL
feature tables, so if you understand how they look, you’ll probably have
an easier time grasping the structure of the Biopython classes.</p>
<p>The key idea about each <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> object is to describe a region on
a parent sequence, typically a <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> object. That region is
described with a location object, typically a range between two
positions (see Section <a class="reference internal" href="#sec-locations"><span class="std std-ref">Positions and locations</span></a> below).</p>
<p>The <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> class has a number of attributes, so first we’ll list
them and their general features, and then later in the chapter work
through examples to show how this applies to a real life example. The
attributes of a SeqFeature are:</p>
<dl>
<dt>.type</dt><dd><p>This is a textual description of the type of feature (for instance,
this will be something like ‘CDS’ or ‘gene’).</p>
</dd>
<dt>.location</dt><dd><p>The location of the <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> on the sequence that you are
dealing with, see Section <a class="reference internal" href="#sec-locations"><span class="std std-ref">Positions and locations</span></a> below. The
<code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> delegates much of its functionality to the location
object, and includes a number of shortcut attributes for properties
of the location:</p>
<dl class="simple">
<dt>.ref</dt><dd><p>shorthand for <code class="docutils literal notranslate"><span class="pre">.location.ref</span></code> – any (different) reference
sequence the location is referring to. Usually just None.</p>
</dd>
<dt>.ref_db</dt><dd><p>shorthand for <code class="docutils literal notranslate"><span class="pre">.location.ref_db</span></code> – specifies the database any
identifier in <code class="docutils literal notranslate"><span class="pre">.ref</span></code> refers to. Usually just None.</p>
</dd>
<dt>.strand</dt><dd><p>shorthand for <code class="docutils literal notranslate"><span class="pre">.location.strand</span></code> – the strand on the sequence
that the feature is located on. For double stranded nucleotide
sequence this may either be <span class="math notranslate nohighlight">\(1\)</span> for the top strand,
<span class="math notranslate nohighlight">\(-1\)</span> for the bottom strand, <span class="math notranslate nohighlight">\(0\)</span> if the strand is
important but is unknown, or <code class="docutils literal notranslate"><span class="pre">None</span></code> if it doesn’t matter. This
is None for proteins, or single stranded sequences.</p>
</dd>
</dl>
</dd>
<dt>.qualifiers</dt><dd><p>This is a Python dictionary of additional information about the
feature. The key is some kind of terse one-word description of what
the information contained in the value is about, and the value is the
actual information. For example, a common key for a qualifier might
be “evidence” and the value might be “computational
(non-experimental).” This is just a way to let the person who is
looking at the feature know that it has not be experimentally
(i. e. in a wet lab) confirmed. Note that other the value will be a
list of strings (even when there is only one string). This is a
reflection of the feature tables in GenBank/EMBL files.</p>
</dd>
<dt>.sub_features</dt><dd><p>This used to be used to represent features with complicated
locations like ‘joins’ in GenBank/EMBL files. This has been
deprecated with the introduction of the <code class="docutils literal notranslate"><span class="pre">CompoundLocation</span></code> object,
and should now be ignored.</p>
</dd>
</dl>
</section>
<section id="positions-and-locations">
<span id="sec-locations"></span><h3>Positions and locations<a class="headerlink" href="#positions-and-locations" title="Link to this heading"></a></h3>
<p>The key idea about each <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> object is to describe a region on
a parent sequence, for which we use a location object, typically
describing a range between two positions. Two try to clarify the
terminology we’re using:</p>
<dl class="simple">
<dt>position</dt><dd><p>This refers to a single position on a sequence, which may be fuzzy
or not. For instance, 5, 20, <code class="docutils literal notranslate"><span class="pre"><100</span></code> and <code class="docutils literal notranslate"><span class="pre">>200</span></code> are all positions.</p>
</dd>
<dt>location</dt><dd><p>A location is region of sequence bounded by some positions. For
instance <code class="docutils literal notranslate"><span class="pre">5..20</span></code> (i. e. 5 to 20) is a location.</p>
</dd>
</dl>
<p>I just mention this because sometimes I get confused between the two.</p>
<section id="simplelocation-object">
<h4>SimpleLocation object<a class="headerlink" href="#simplelocation-object" title="Link to this heading"></a></h4>
<p>Unless you work with eukaryotic genes, most <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> locations are
extremely simple - you just need start and end coordinates and a strand.
That’s essentially all the basic <code class="docutils literal notranslate"><span class="pre">SimpleLocation</span></code> object does.</p>
<p>In practice of course, things can be more complicated. First of all we
have to handle compound locations made up of several regions. Secondly,
the positions themselves may be fuzzy (inexact).</p>
</section>
<section id="compoundlocation-object">
<h4>CompoundLocation object<a class="headerlink" href="#compoundlocation-object" title="Link to this heading"></a></h4>
<p>Biopython 1.62 introduced the <code class="docutils literal notranslate"><span class="pre">CompoundLocation</span></code> as part of a
restructuring of how complex locations made up of multiple regions are
represented. The main usage is for handling ‘join’ locations in
EMBL/GenBank files.</p>
</section>
<section id="fuzzy-positions">
<h4>Fuzzy Positions<a class="headerlink" href="#fuzzy-positions" title="Link to this heading"></a></h4>
<p>So far we’ve only used simple positions. One complication in dealing
with feature locations comes in the positions themselves. In biology
many times things aren’t entirely certain (as much as us wet lab
biologists try to make them certain!). For instance, you might do a
dinucleotide priming experiment and discover that the start of mRNA
transcript starts at one of two sites. This is very useful information,
but the complication comes in how to represent this as a position. To
help us deal with this, we have the concept of fuzzy positions.
Basically there are several types of fuzzy positions, so we have five
classes to deal with them:</p>
<dl class="simple">
<dt>ExactPosition</dt><dd><p>As its name suggests, this class represents a position which is
specified as exact along the sequence. This is represented as just a
number, and you can get the position by looking at the <code class="docutils literal notranslate"><span class="pre">position</span></code>
attribute of the object.</p>
</dd>
<dt>BeforePosition</dt><dd><p>This class represents a fuzzy position that occurs prior to some
specified site. In GenBank/EMBL notation, this is represented as
something like <code class="docutils literal notranslate"><span class="pre"><13</span></code>, signifying that the real position
is located somewhere less than 13. To get the specified upper
boundary, look at the <code class="docutils literal notranslate"><span class="pre">position</span></code> attribute of the object.</p>
</dd>
<dt>AfterPosition</dt><dd><p>Contrary to <code class="docutils literal notranslate"><span class="pre">BeforePosition</span></code>, this class represents a position
that occurs after some specified site. This is represented in GenBank
as <code class="docutils literal notranslate"><span class="pre">>13</span></code>, and like <code class="docutils literal notranslate"><span class="pre">BeforePosition</span></code>, you get the
boundary number by looking at the <code class="docutils literal notranslate"><span class="pre">position</span></code> attribute of the
object.</p>
</dd>
<dt>WithinPosition</dt><dd><p>Occasionally used for GenBank/EMBL locations, this class models a
position which occurs somewhere between two specified nucleotides. In
GenBank/EMBL notation, this would be represented as <code class="docutils literal notranslate"><span class="pre">(1.5)</span></code>, to
represent that the position is somewhere within the range 1 to 5.</p>
</dd>
<dt>OneOfPosition</dt><dd><p>Occasionally used for GenBank/EMBL locations, this class deals with
a position where several possible values exist, for instance you
could use this if the start codon was unclear and there where two
candidates for the start of the gene. Alternatively, that might be
handled explicitly as two related gene features.</p>
</dd>
<dt>UnknownPosition</dt><dd><p>This class deals with a position of unknown location. This is not
used in GenBank/EMBL, but corresponds to the ‘?’ feature coordinate
used in UniProt.</p>
</dd>
</dl>
<p>Here’s an example where we create a location with fuzzy end points:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqFeature</span>
<span class="gp">>>> </span><span class="n">start_pos</span> <span class="o">=</span> <span class="n">SeqFeature</span><span class="o">.</span><span class="n">AfterPosition</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">end_pos</span> <span class="o">=</span> <span class="n">SeqFeature</span><span class="o">.</span><span class="n">BetweenPosition</span><span class="p">(</span><span class="mi">9</span><span class="p">,</span> <span class="n">left</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span> <span class="n">right</span><span class="o">=</span><span class="mi">9</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">my_location</span> <span class="o">=</span> <span class="n">SeqFeature</span><span class="o">.</span><span class="n">SimpleLocation</span><span class="p">(</span><span class="n">start_pos</span><span class="p">,</span> <span class="n">end_pos</span><span class="p">)</span>
</pre></div>
</div>
<p>Note that the details of some of the fuzzy-locations changed in
Biopython 1.59, in particular for BetweenPosition and WithinPosition you
must now make it explicit which integer position should be used for
slicing etc. For a start position this is generally the lower (left)
value, while for an end position this would generally be the higher
(right) value.</p>
<p>If you print out a <code class="docutils literal notranslate"><span class="pre">SimpleLocation</span></code> object, you can get a nice
representation of the information:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">my_location</span><span class="p">)</span>
<span class="go">[>5:(8^9)]</span>
</pre></div>
</div>
<p>We can access the fuzzy start and end positions using the start and end
attributes of the location:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">my_location</span><span class="o">.</span><span class="n">start</span>
<span class="go">AfterPosition(5)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">my_location</span><span class="o">.</span><span class="n">start</span><span class="p">)</span>
<span class="go">>5</span>
<span class="gp">>>> </span><span class="n">my_location</span><span class="o">.</span><span class="n">end</span>
<span class="go">BetweenPosition(9, left=8, right=9)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">my_location</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
<span class="go">(8^9)</span>
</pre></div>
</div>
<p>If you don’t want to deal with fuzzy positions and just want numbers,
they are actually subclasses of integers so should work like integers:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">int</span><span class="p">(</span><span class="n">my_location</span><span class="o">.</span><span class="n">start</span><span class="p">)</span>
<span class="go">5</span>
<span class="gp">>>> </span><span class="nb">int</span><span class="p">(</span><span class="n">my_location</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
<span class="go">9</span>
</pre></div>
</div>
<p>Similarly, to make it easy to create a position without worrying about
fuzzy positions, you can just pass in numbers to the <code class="docutils literal notranslate"><span class="pre">FeaturePosition</span></code>
constructors, and you’ll get back out <code class="docutils literal notranslate"><span class="pre">ExactPosition</span></code> objects:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">exact_location</span> <span class="o">=</span> <span class="n">SeqFeature</span><span class="o">.</span><span class="n">SimpleLocation</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">9</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">exact_location</span><span class="p">)</span>
<span class="go">[5:9]</span>
<span class="gp">>>> </span><span class="n">exact_location</span><span class="o">.</span><span class="n">start</span>
<span class="go">ExactPosition(5)</span>
<span class="gp">>>> </span><span class="nb">int</span><span class="p">(</span><span class="n">exact_location</span><span class="o">.</span><span class="n">start</span><span class="p">)</span>
<span class="go">5</span>
</pre></div>
</div>
<p>That is most of the nitty gritty about dealing with fuzzy positions in
Biopython. It has been designed so that dealing with fuzziness is not
that much more complicated than dealing with exact positions, and
hopefully you find that true!</p>
</section>
<section id="location-testing">
<h4>Location testing<a class="headerlink" href="#location-testing" title="Link to this heading"></a></h4>
<p>You can use the Python keyword <code class="docutils literal notranslate"><span class="pre">in</span></code> with a <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> or location
object to see if the base/residue for a parent coordinate is within the
feature/location or not.</p>
<p>For example, suppose you have a SNP of interest and you want to know
which features this SNP is within, and lets suppose this SNP is at index
4350 (Python counting!). Here is a simple brute force solution where we
just check all the features one by one in a loop:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">my_snp</span> <span class="o">=</span> <span class="mi">4350</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">"NC_005816.gb"</span><span class="p">,</span> <span class="s2">"genbank"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="n">record</span><span class="o">.</span><span class="n">features</span><span class="p">:</span>
<span class="gp">... </span> <span class="k">if</span> <span class="n">my_snp</span> <span class="ow">in</span> <span class="n">feature</span><span class="p">:</span>
<span class="gp">... </span> <span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">feature</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">feature</span><span class="o">.</span><span class="n">qualifiers</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"db_xref"</span><span class="p">)))</span>
<span class="gp">...</span>
<span class="go">source ['taxon:229193']</span>
<span class="go">gene ['GeneID:2767712']</span>
<span class="go">CDS ['GI:45478716', 'GeneID:2767712']</span>
</pre></div>
</div>
<p>Note that gene and CDS features from GenBank or EMBL files defined with
joins are the union of the exons – they do not cover any introns.</p>
</section>
</section>
<section id="sequence-described-by-a-feature-or-location">
<h3>Sequence described by a feature or location<a class="headerlink" href="#sequence-described-by-a-feature-or-location" title="Link to this heading"></a></h3>
<p>A <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> or location object doesn’t directly contain a sequence,
instead the location (see Section <a class="reference internal" href="#sec-locations"><span class="std std-ref">Positions and locations</span></a>) describes
how to get this from the parent sequence. For example consider a (short)
gene sequence with location <code class="docutils literal notranslate"><span class="pre">5:18</span></code> on the reverse strand, which in
GenBank/EMBL notation using 1-based counting would be
<code class="docutils literal notranslate"><span class="pre">complement(6..18)</span></code>, like this:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqFeature</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqFeature</span><span class="p">,</span> <span class="n">SimpleLocation</span>
<span class="gp">>>> </span><span class="n">seq</span> <span class="o">=</span> <span class="n">Seq</span><span class="p">(</span><span class="s2">"ACCGAGACGGCAAAGGCTAGCATAGGTATGAGACTTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">feature</span> <span class="o">=</span> <span class="n">SeqFeature</span><span class="p">(</span><span class="n">SimpleLocation</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">18</span><span class="p">,</span> <span class="n">strand</span><span class="o">=-</span><span class="mi">1</span><span class="p">),</span> <span class="nb">type</span><span class="o">=</span><span class="s2">"gene"</span><span class="p">)</span>
</pre></div>
</div>
<p>You could take the parent sequence, slice it to extract <code class="docutils literal notranslate"><span class="pre">5:18</span></code>, and then
take the reverse complement. The feature location’s start and end are
integer-like so this works:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">feature_seq</span> <span class="o">=</span> <span class="n">seq</span><span class="p">[</span><span class="n">feature</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">start</span> <span class="p">:</span> <span class="n">feature</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">end</span><span class="p">]</span><span class="o">.</span><span class="n">reverse_complement</span><span class="p">()</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">feature_seq</span><span class="p">)</span>
<span class="go">AGCCTTTGCCGTC</span>
</pre></div>
</div>
<p>This is a simple example so this isn’t too bad – however once you have
to deal with compound features (joins) this is rather messy. Instead,
the <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> object has an <code class="docutils literal notranslate"><span class="pre">extract</span></code> method to take care of all
this (and since Biopython 1.78 can handle trans-splicing by supplying a
dictionary of referenced sequences):</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">feature_seq</span> <span class="o">=</span> <span class="n">feature</span><span class="o">.</span><span class="n">extract</span><span class="p">(</span><span class="n">seq</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">feature_seq</span><span class="p">)</span>
<span class="go">AGCCTTTGCCGTC</span>
</pre></div>
</div>
<p>The length of a <code class="docutils literal notranslate"><span class="pre">SeqFeature</span></code> or location matches that of the region of
sequence it describes.</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">feature_seq</span><span class="p">))</span>
<span class="go">13</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">feature</span><span class="p">))</span>
<span class="go">13</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">feature</span><span class="o">.</span><span class="n">location</span><span class="p">))</span>
<span class="go">13</span>
</pre></div>
</div>
<p>For <code class="docutils literal notranslate"><span class="pre">SimpleLocation</span></code> objects the length is just the difference between
the start and end positions. However, for a <code class="docutils literal notranslate"><span class="pre">CompoundLocation</span></code> the
length is the sum of the constituent regions.</p>
</section>
</section>
<section id="comparison">
<h2>Comparison<a class="headerlink" href="#comparison" title="Link to this heading"></a></h2>
<p>The <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> objects can be very complex, but here’s a simple
example:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqRecord</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="gp">>>> </span><span class="n">record1</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="s2">"ACGT"</span><span class="p">),</span> <span class="nb">id</span><span class="o">=</span><span class="s2">"test"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">record2</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="s2">"ACGT"</span><span class="p">),</span> <span class="nb">id</span><span class="o">=</span><span class="s2">"test"</span><span class="p">)</span>
</pre></div>
</div>
<p>What happens when you try to compare these “identical” records?</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record1</span> <span class="o">==</span> <span class="n">record2</span>
</pre></div>
</div>
<p>Perhaps surprisingly older versions of Biopython would use Python’s
default object comparison for the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>, meaning
<code class="docutils literal notranslate"><span class="pre">record1</span> <span class="pre">==</span> <span class="pre">record2</span></code> would only return <code class="docutils literal notranslate"><span class="pre">True</span></code> if these variables
pointed at the same object in memory. In this example,
<code class="docutils literal notranslate"><span class="pre">record1</span> <span class="pre">==</span> <span class="pre">record2</span></code> would have returned <code class="docutils literal notranslate"><span class="pre">False</span></code> here!</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record1</span> <span class="o">==</span> <span class="n">record2</span> <span class="c1"># on old versions of Biopython!</span>
<span class="go">False</span>
</pre></div>
</div>
<p>As of Biopython 1.67, <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> comparison like
<code class="docutils literal notranslate"><span class="pre">record1</span> <span class="pre">==</span> <span class="pre">record2</span></code> will instead raise an explicit error to avoid
people being caught out by this:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record1</span> <span class="o">==</span> <span class="n">record2</span>
<span class="gt">Traceback (most recent call last):</span>
<span class="c">...</span>
<span class="gr">NotImplementedError</span>: <span class="n">SeqRecord comparison is deliberately not implemented. Explicitly compare the attributes of interest.</span>
</pre></div>
</div>
<p>Instead you should check the attributes you are interested in, for
example the identifier and the sequence:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">record1</span><span class="o">.</span><span class="n">id</span> <span class="o">==</span> <span class="n">record2</span><span class="o">.</span><span class="n">id</span>
<span class="go">True</span>
<span class="gp">>>> </span><span class="n">record1</span><span class="o">.</span><span class="n">seq</span> <span class="o">==</span> <span class="n">record2</span><span class="o">.</span><span class="n">seq</span>
<span class="go">True</span>
</pre></div>
</div>
<p>Beware that comparing complex objects quickly gets complicated (see also
Section <a class="reference internal" href="chapter_seq_objects.html#sec-seq-comparison"><span class="std std-ref">Comparing Seq objects</span></a>).</p>
</section>
<section id="references">
<h2>References<a class="headerlink" href="#references" title="Link to this heading"></a></h2>
<p>Another common annotation related to a sequence is a reference to a
journal or other published work dealing with the sequence. We have a
fairly simple way of representing a Reference in Biopython – we have a
<code class="docutils literal notranslate"><span class="pre">Bio.SeqFeature.Reference</span></code> class that stores the relevant information
about a reference as attributes of an object.</p>
<p>The attributes include things that you would expect to see in a
reference like <code class="docutils literal notranslate"><span class="pre">journal</span></code>, <code class="docutils literal notranslate"><span class="pre">title</span></code> and <code class="docutils literal notranslate"><span class="pre">authors</span></code>. Additionally, it
also can hold the <code class="docutils literal notranslate"><span class="pre">medline_id</span></code> and <code class="docutils literal notranslate"><span class="pre">pubmed_id</span></code> and a <code class="docutils literal notranslate"><span class="pre">comment</span></code>
about the reference. These are all accessed simply as attributes of the
object.</p>
<p>A reference also has a <code class="docutils literal notranslate"><span class="pre">location</span></code> object so that it can specify a
particular location on the sequence that the reference refers to. For
instance, you might have a journal that is dealing with a particular
gene located on a BAC, and want to specify that it only refers to this
position exactly. The <code class="docutils literal notranslate"><span class="pre">location</span></code> is a potentially fuzzy location, as
described in section <a class="reference internal" href="#sec-locations"><span class="std std-ref">Positions and locations</span></a>.</p>
<p>Any reference objects are stored as a list in the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> object’s
<code class="docutils literal notranslate"><span class="pre">annotations</span></code> dictionary under the key “references”. That’s all there
is too it. References are meant to be easy to deal with, and hopefully
general enough to cover lots of usage cases.</p>
</section>
<section id="the-format-method">
<span id="sec-seqrecord-format"></span><h2>The format method<a class="headerlink" href="#the-format-method" title="Link to this heading"></a></h2>
<p>The <code class="docutils literal notranslate"><span class="pre">format()</span></code> method of the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> class gives a string
containing your record formatted using one of the output file formats
supported by <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code>, such as FASTA:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.Seq</span><span class="w"> </span><span class="kn">import</span> <span class="n">Seq</span>
<span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio.SeqRecord</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqRecord</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqRecord</span><span class="p">(</span>
<span class="gp">... </span> <span class="n">Seq</span><span class="p">(</span>
<span class="gp">... </span> <span class="s2">"MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD"</span>
<span class="gp">... </span> <span class="s2">"GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK"</span>
<span class="gp">... </span> <span class="s2">"NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM"</span>
<span class="gp">... </span> <span class="s2">"SSAC"</span>
<span class="gp">... </span> <span class="p">),</span>
<span class="gp">... </span> <span class="nb">id</span><span class="o">=</span><span class="s2">"gi|14150838|gb|AAK54648.1|AF376133_1"</span><span class="p">,</span>
<span class="gp">... </span> <span class="n">description</span><span class="o">=</span><span class="s2">"chalcone synthase [Cucumis sativus]"</span><span class="p">,</span>
<span class="gp">... </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">format</span><span class="p">(</span><span class="s2">"fasta"</span><span class="p">))</span>
</pre></div>
</div>
<p>which should give:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="go">>gi|14150838|gb|AAK54648.1|AF376133_1 chalcone synthase [Cucumis sativus]</span>
<span class="go">MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD</span>
<span class="go">GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK</span>
<span class="go">NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM</span>
<span class="go">SSAC</span>
</pre></div>
</div>
<p>This <code class="docutils literal notranslate"><span class="pre">format</span></code> method takes a single mandatory argument, a lower case
string which is supported by <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code> as an output format (see
Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a>). However, some of the file
formats <code class="docutils literal notranslate"><span class="pre">Bio.SeqIO</span></code> can write to <em>require</em> more than one record
(typically the case for multiple sequence alignment formats), and thus
won’t work via this <code class="docutils literal notranslate"><span class="pre">format()</span></code> method. See also
Section <a class="reference internal" href="chapter_seqio.html#sec-bio-seqio-and-stringio"><span class="std std-ref">Getting your SeqRecord objects as formatted strings</span></a>.</p>
</section>
<section id="slicing-a-seqrecord">
<span id="sec-seqrecord-slicing"></span><h2>Slicing a SeqRecord<a class="headerlink" href="#slicing-a-seqrecord" title="Link to this heading"></a></h2>
<p>You can slice a <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>, to give you a new <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> covering
just part of the sequence. What is important here is that any per-letter
annotations are also sliced, and any features which fall completely
within the new sequence are preserved (with their locations adjusted).</p>
<p>For example, taking the same GenBank file used earlier:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">"NC_005816.gb"</span><span class="p">,</span> <span class="s2">"genbank"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">record</span>
<span class="go">SeqRecord(seq=Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG'), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=['Project:58037'])</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
<span class="go">9609</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">features</span><span class="p">)</span>
<span class="go">41</span>
</pre></div>
</div>
<p>For this example we’re going to focus in on the <code class="docutils literal notranslate"><span class="pre">pim</span></code> gene,
<code class="docutils literal notranslate"><span class="pre">YP_pPCP05</span></code>. If you have a look at the GenBank file directly you’ll
find this gene/CDS has location string <code class="docutils literal notranslate"><span class="pre">4343..4780</span></code>, or in Python
counting <code class="docutils literal notranslate"><span class="pre">4342:4780</span></code>. From looking at the file you can work out that
these are the twelfth and thirteenth entries in the file, so in Python
zero-based counting they are entries <span class="math notranslate nohighlight">\(11\)</span> and <span class="math notranslate nohighlight">\(12\)</span> in the
<code class="docutils literal notranslate"><span class="pre">features</span></code> list:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></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">features</span><span class="p">[</span><span class="mi">20</span><span class="p">])</span>
<span class="go">type: gene</span>
<span class="go">location: [4342:4780](+)</span>
<span class="go">qualifiers:</span>
<span class="go"> Key: db_xref, Value: ['GeneID:2767712']</span>
<span class="go"> Key: gene, Value: ['pim']</span>
<span class="go"> Key: locus_tag, Value: ['YP_pPCP05']</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">features</span><span class="p">[</span><span class="mi">21</span><span class="p">])</span>
<span class="go">type: CDS</span>
<span class="go">location: [4342:4780](+)</span>
<span class="go">qualifiers:</span>
<span class="go"> Key: codon_start, Value: ['1']</span>
<span class="go"> Key: db_xref, Value: ['GI:45478716', 'GeneID:2767712']</span>
<span class="go"> Key: gene, Value: ['pim']</span>
<span class="go"> Key: locus_tag, Value: ['YP_pPCP05']</span>
<span class="go"> Key: note, Value: ['similar to many previously sequenced pesticin immunity protein entries of Yersinia pestis plasmid pPCP, e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)']</span>
<span class="go"> Key: product, Value: ['pesticin immunity protein']</span>
<span class="go"> Key: protein_id, Value: ['NP_995571.1']</span>
<span class="go"> Key: transl_table, Value: ['11']</span>
<span class="go"> Key: translation, Value: ['MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGNSLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFEDFSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH']</span>
</pre></div>
</div>
<p>Let’s slice this parent record from 4300 to 4800 (enough to include the
<code class="docutils literal notranslate"><span class="pre">pim</span></code> gene/CDS), and see how many features we get:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sub_record</span> <span class="o">=</span> <span class="n">record</span><span class="p">[</span><span class="mi">4300</span><span class="p">:</span><span class="mi">4800</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">sub_record</span>
<span class="go">SeqRecord(seq=Seq('ATAAATAGATTATTCCAAATAATTTATTTATGTAAGAACAGGATGGGAGGGGGA...TTA'), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=[])</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">sub_record</span><span class="p">)</span>
<span class="go">500</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">sub_record</span><span class="o">.</span><span class="n">features</span><span class="p">)</span>
<span class="go">2</span>
</pre></div>
</div>
<p>Our sub-record just has two features, the gene and CDS entries for
<code class="docutils literal notranslate"><span class="pre">YP_pPCP05</span></code>:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">sub_record</span><span class="o">.</span><span class="n">features</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="go">type: gene</span>
<span class="go">location: [42:480](+)</span>
<span class="go">qualifiers:</span>
<span class="go"> Key: db_xref, Value: ['GeneID:2767712']</span>
<span class="go"> Key: gene, Value: ['pim']</span>
<span class="go"> Key: locus_tag, Value: ['YP_pPCP05']</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">sub_record</span><span class="o">.</span><span class="n">features</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="go">type: CDS</span>
<span class="go">location: [42:480](+)</span>
<span class="go">qualifiers:</span>
<span class="go"> Key: codon_start, Value: ['1']</span>
<span class="go"> Key: db_xref, Value: ['GI:45478716', 'GeneID:2767712']</span>
<span class="go"> Key: gene, Value: ['pim']</span>
<span class="go"> Key: locus_tag, Value: ['YP_pPCP05']</span>
<span class="go"> Key: note, Value: ['similar to many previously sequenced pesticin immunity protein entries of Yersinia pestis plasmid pPCP, e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)']</span>
<span class="go"> Key: product, Value: ['pesticin immunity protein']</span>
<span class="go"> Key: protein_id, Value: ['NP_995571.1']</span>
<span class="go"> Key: transl_table, Value: ['11']</span>
<span class="go"> Key: translation, Value: ['MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGNSLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFEDFSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH']</span>
</pre></div>
</div>
<p>Notice that their locations have been adjusted to reflect the new parent
sequence!</p>
<p>While Biopython has done something sensible and hopefully intuitive with
the features (and any per-letter annotation), for the other annotation
it is impossible to know if this still applies to the sub-sequence or
not. To avoid guessing, with the exception of the molecule type, the
<code class="docutils literal notranslate"><span class="pre">.annotations</span></code> and <code class="docutils literal notranslate"><span class="pre">.dbxrefs</span></code> are omitted from the sub-record, and
it is up to you to transfer any relevant information as appropriate.</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">annotations</span>
<span class="go">{'molecule_type': 'DNA'}</span>
<span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">dbxrefs</span>
<span class="go">[]</span>
</pre></div>
</div>
<p>You may wish to preserve other entries like the organism? Beware of
copying the entire annotations dictionary as in this case your partial
sequence is no longer circular DNA - it is now linear:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="s2">"topology"</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"linear"</span>
</pre></div>
</div>
<p>The same point could be made about the record <code class="docutils literal notranslate"><span class="pre">id</span></code>, <code class="docutils literal notranslate"><span class="pre">name</span></code> and
<code class="docutils literal notranslate"><span class="pre">description</span></code>, but for practicality these are preserved:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">id</span>
<span class="go">'NC_005816.1'</span>
<span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">name</span>
<span class="go">'NC_005816'</span>
<span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">description</span>
<span class="go">'Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence'</span>
</pre></div>
</div>
<p>This illustrates the problem nicely though, our new sub-record is <em>not</em>
the complete sequence of the plasmid, so the description is wrong! Let’s
fix this and then view the sub-record as a reduced GenBank file using
the <code class="docutils literal notranslate"><span class="pre">format</span></code> method described above in
Section <a class="reference internal" href="#sec-seqrecord-format"><span class="std std-ref">The format method</span></a>:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sub_record</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="p">(</span>
<span class="gp">... </span> <span class="s2">"Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, partial"</span>
<span class="gp">... </span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">sub_record</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"genbank"</span><span class="p">)[:</span><span class="mi">200</span><span class="p">]</span> <span class="o">+</span> <span class="s2">"..."</span><span class="p">)</span>
<span class="go">LOCUS NC_005816 500 bp DNA linear UNK 01-JAN-1980</span>
<span class="go">DEFINITION Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, partial.</span>
<span class="go">ACCESSION NC_005816</span>
<span class="go">VERSION NC_0058...</span>
</pre></div>
</div>
<p>See
Sections <a class="reference internal" href="chapter_cookbook.html#sec-fastq-slicing-off-primer"><span class="std std-ref">Trimming off primer sequences</span></a>
and <a class="reference internal" href="chapter_cookbook.html#sec-fastq-slicing-off-adaptor"><span class="std std-ref">Trimming off adaptor sequences</span></a>
for some FASTQ examples where the per-letter annotations (the read
quality scores) are also sliced.</p>
</section>
<section id="adding-seqrecord-objects">
<span id="sec-seqrecord-addition"></span><h2>Adding SeqRecord objects<a class="headerlink" href="#adding-seqrecord-objects" title="Link to this heading"></a></h2>
<p>You can add <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> objects together, giving a new <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code>.
What is important here is that any common per-letter annotations are
also added, all the features are preserved (with their locations
adjusted), and any other common annotation is also kept (like the id,
name and description).</p>
<p>For an example with per-letter annotation, we’ll use the first record in
a FASTQ file. Chapter <a class="reference internal" href="chapter_seqio.html#chapter-seqio"><span class="std std-ref">Sequence Input/Output</span></a> will explain
the <code class="docutils literal notranslate"><span class="pre">SeqIO</span></code> functions:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">SeqIO</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="s2">"example.fastq"</span><span class="p">,</span> <span class="s2">"fastq"</span><span class="p">))</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
<span class="go">25</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">seq</span><span class="p">)</span>
<span class="go">CCCTTCTTGTCTTCAGCGTTTCTCC</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">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">])</span>
<span class="go">[26, 26, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 26, 26, 26, 26, 26, 26, 26, 23, 23]</span>
</pre></div>
</div>
<p>Let’s suppose this was Roche 454 data, and that from other information
you think the <code class="docutils literal notranslate"><span class="pre">TTT</span></code> should be only <code class="docutils literal notranslate"><span class="pre">TT</span></code>. We can make a new edited
record by first slicing the <code class="docutils literal notranslate"><span class="pre">SeqRecord</span></code> before and after the “extra”
third <code class="docutils literal notranslate"><span class="pre">T</span></code>:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">left</span> <span class="o">=</span> <span class="n">record</span><span class="p">[:</span><span class="mi">20</span><span class="p">]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">left</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span>
<span class="go">CCCTTCTTGTCTTCAGCGTT</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">left</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">])</span>
<span class="go">[26, 26, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 26, 26, 26, 26]</span>
<span class="gp">>>> </span><span class="n">right</span> <span class="o">=</span> <span class="n">record</span><span class="p">[</span><span class="mi">21</span><span class="p">:]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">right</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span>
<span class="go">CTCC</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">right</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">])</span>
<span class="go">[26, 26, 23, 23]</span>
</pre></div>
</div>
<p>Now add the two parts together:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">edited</span> <span class="o">=</span> <span class="n">left</span> <span class="o">+</span> <span class="n">right</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">edited</span><span class="p">)</span>
<span class="go">24</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">edited</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span>
<span class="go">CCCTTCTTGTCTTCAGCGTTCTCC</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">edited</span><span class="o">.</span><span class="n">letter_annotations</span><span class="p">[</span><span class="s2">"phred_quality"</span><span class="p">])</span>
<span class="go">[26, 26, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 26, 26, 26, 26, 26, 26, 23, 23]</span>
</pre></div>
</div>
<p>Easy and intuitive? We hope so! You can make this shorter with just:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">edited</span> <span class="o">=</span> <span class="n">record</span><span class="p">[:</span><span class="mi">20</span><span class="p">]</span> <span class="o">+</span> <span class="n">record</span><span class="p">[</span><span class="mi">21</span><span class="p">:]</span>
</pre></div>
</div>
<p>Now, for an example with features, we’ll use a GenBank file. Suppose you
have a circular genome:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SeqIO</span>
<span class="gp">>>> </span><span class="n">record</span> <span class="o">=</span> <span class="n">SeqIO</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s2">"NC_005816.gb"</span><span class="p">,</span> <span class="s2">"genbank"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">record</span>
<span class="go">SeqRecord(seq=Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG...CTG'), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=['Project:58037'])</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
<span class="go">9609</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">features</span><span class="p">)</span>
<span class="go">41</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">dbxrefs</span>
<span class="go">['Project:58037']</span>
<span class="gp">>>> </span><span class="n">record</span><span class="o">.</span><span class="n">annotations</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
<span class="go">dict_keys(['molecule_type', 'topology', 'data_file_division', 'date', 'accessions', 'sequence_version', 'gi', 'keywords', 'source', 'organism', 'taxonomy', 'references', 'comment'])</span>
</pre></div>
</div>
<p>You can shift the origin like this:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">shifted</span> <span class="o">=</span> <span class="n">record</span><span class="p">[</span><span class="mi">2000</span><span class="p">:]</span> <span class="o">+</span> <span class="n">record</span><span class="p">[:</span><span class="mi">2000</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">shifted</span>
<span class="go">SeqRecord(seq=Seq('GATACGCAGTCATATTTTTTACACAATTCTCTAATCCCGACAAGGTCGTAGGTC...GGA'), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence', dbxrefs=[])</span>
<span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">shifted</span><span class="p">)</span>
<span class="go">9609</span>
</pre></div>
</div>
<p>Note that this isn’t perfect in that some annotation like the database
cross references, all the annotations except molecule type, and one of
the features (the source feature) have been lost:</p>
<div class="highlight-pycon notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">len</span><span class="p">(</span><span class="n">shifted</span><span class="o">.</span><span class="n">features</span><span class="p">)</span>
<span class="go">40</span>
<span class="gp">>>> </span><span class="n">shifted</span><span class="o">.</span><span class="n">dbxrefs</span>
<span class="go">[]</span>
<span class="gp">>>> </span><span class="n">shifted</span><span class="o">.</span><span class="n">annotations</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
<span class="go">dict_keys(['molecule_type'])</span>
</pre></div>