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<a href="Bio-module.html">Package Bio</a> ::
Package Graphics
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<h1 class="epydoc">Source Code for <a href="Bio.Graphics-module.html">Package Bio.Graphics</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2008 by Michiel de Hoon. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2008-2009 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment">################################################################################</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.Graphics offsers several graphical ouputs, all using ReportLab."""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># Check if ReportLab is installed.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">reportlab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">r</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">r</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class Bio.MissingPythonDependencyError=Bio.MissingPythonDependencyError-class.html"><a title="Bio.MissingPythonDependencyError" class="py-name" href="#" onclick="return doclink('link-1', 'MissingPythonDependencyError', 'link-1');">MissingPythonDependencyError</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-2" class="py-name"><a title="Bio.MissingPythonDependencyError" class="py-name" href="#" onclick="return doclink('link-2', 'MissingPythonDependencyError', 'link-1');">MissingPythonDependencyError</a></tt><tt class="py-op">(</tt> \ </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-string">"Please install ReportLab if you want "</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-string">"to use Bio.Graphics. You can find ReportLab at "</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-string">"http://www.reportlab.org/downloads.html"</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-comment"># The following code is to allow all the Bio.Graphics</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-comment"># code to deal with the different ReportLab renderers</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"># and the API quirks consistently.</tt> </tt>
<a name="_write"></a><div id="_write-def"><a name="L23"></a><tt class="py-lineno">23</tt> <a class="py-toggle" href="#" id="_write-toggle" onclick="return toggle('_write');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics-module.html#_write">_write</a><tt class="py-op">(</tt><tt class="py-param">drawing</tt><tt class="py-op">,</tt> <tt class="py-param">output_file</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">dpi</tt><tt class="py-op">=</tt><tt class="py-number">72</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_write-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_write-expanded"><a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-docstring">"""Helper function to standize output to files (PRIVATE).</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> Writes the provided drawing out to a file in a prescribed format.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> drawing - suitable ReportLab drawing object.</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> output_file - a handle to write to, or a filename to write to.</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> format - String indicating output format, one of PS, PDF, SVG,</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> or provided the ReportLab renderPM module is installed,</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> one of the bitmap formats JPG, BMP, GIF, PNG, TIFF or TIFF.</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> The format can be given in any case.</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> dpi - Resolution (dots per inch) for bitmap formats.</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> No return value.</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt> <tt class="py-keyword">import</tt> <tt class="py-name">renderPS</tt><tt class="py-op">,</tt> <tt class="py-name">renderPDF</tt><tt class="py-op">,</tt> <tt class="py-name">renderSVG</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Variable Bio.Graphics.GenomeDiagram._Diagram.renderPM=Bio.Graphics.GenomeDiagram._Diagram-module.html#renderPM"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-3', 'renderPM', 'link-3');">renderPM</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-comment">#This is an optional part of ReportLab, so may not be installed.</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-comment">#We'll raise a missing dependency error if rendering to a</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-comment">#bitmap format is attempted.</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-4', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">formatdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'PS'</tt><tt class="py-op">:</tt> <tt class="py-name">renderPS</tt><tt class="py-op">,</tt> <tt class="py-string">'EPS'</tt><tt class="py-op">:</tt> <tt class="py-name">renderPS</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-comment"># not sure which you actually get, PS or EPS, but</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-comment"># GenomeDiagram used PS while other modules used EPS.</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-string">'PDF'</tt><tt class="py-op">:</tt> <tt class="py-name">renderPDF</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-string">'SVG'</tt><tt class="py-op">:</tt> <tt class="py-name">renderSVG</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-string">'JPG'</tt><tt class="py-op">:</tt> <tt id="link-5" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-5', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-string">'BMP'</tt><tt class="py-op">:</tt> <tt id="link-6" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-6', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-string">'GIF'</tt><tt class="py-op">:</tt> <tt id="link-7" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-7', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-string">'PNG'</tt><tt class="py-op">:</tt> <tt id="link-8" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-8', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-string">'TIFF'</tt><tt class="py-op">:</tt> <tt id="link-9" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-9', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">,</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-string">'TIF'</tt><tt class="py-op">:</tt> <tt id="link-10" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-10', 'renderPM', 'link-3');">renderPM</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-comment">#If output is not a string, then .upper() will trigger</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-comment">#an attribute error...</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-name">drawmethod</tt> <tt class="py-op">=</tt> <tt class="py-name">formatdict</tt><tt class="py-op">[</tt><tt id="link-11" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-11', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Seq.Seq.upper()=Bio.Seq.Seq-class.html#upper,Method Bio.Seq.UnknownSeq.upper()=Bio.Seq.UnknownSeq-class.html#upper,Method Bio.SeqRecord.SeqRecord.upper()=Bio.SeqRecord.SeqRecord-class.html#upper"><a title="Bio.Seq.Seq.upper
Bio.Seq.UnknownSeq.upper
Bio.SeqRecord.SeqRecord.upper" class="py-name" href="#" onclick="return doclink('link-12', 'upper', 'link-12');">upper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-comment"># select drawing method</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-op">(</tt><tt class="py-name">KeyError</tt><tt class="py-op">,</tt><tt class="py-name">AttributeError</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Output format should be one of %s"</tt> \ </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-string">", "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">formatdict</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">drawmethod</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-comment">#i.e. We wanted renderPM but it isn't installed</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-comment">#See the import at the top of the function.</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name"><a title="Bio.MissingPythonDependencyError" class="py-name" href="#" onclick="return doclink('link-14', 'MissingPythonDependencyError', 'link-1');">MissingPythonDependencyError</a></tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-15" class="py-name"><a title="Bio.MissingPythonDependencyError" class="py-name" href="#" onclick="return doclink('link-15', 'MissingPythonDependencyError', 'link-1');">MissingPythonDependencyError</a></tt><tt class="py-op">(</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-string">"Please install ReportLab's renderPM module"</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">drawmethod</tt> <tt class="py-op">==</tt> <tt id="link-16" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-16', 'renderPM', 'link-3');">renderPM</a></tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-comment">#This has a different API to the other render objects</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">drawmethod</tt><tt class="py-op">.</tt><tt class="py-name">drawToFile</tt><tt class="py-op">(</tt><tt class="py-name">drawing</tt><tt class="py-op">,</tt> <tt class="py-name">output_file</tt><tt class="py-op">,</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-17', 'format', 'link-11');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">dpi</tt><tt class="py-op">=</tt><tt class="py-name">dpi</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">drawmethod</tt><tt class="py-op">.</tt><tt class="py-name">drawToFile</tt><tt class="py-op">(</tt><tt class="py-name">drawing</tt><tt class="py-op">,</tt> <tt class="py-name">output_file</tt><tt class="py-op">)</tt> </tt>
</div><a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> </tt><script type="text/javascript">
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