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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Affy-module.html">Package Affy</a> ::
Module CelFile
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<h1 class="epydoc">Source Code for <a href="Bio.Affy.CelFile-module.html">Module Bio.Affy.CelFile</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 2004 by Harry Zuzan. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</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="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">Classes for accessing the information in Affymetrix cel files.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">read Read a cel file and store its contents in a Record</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Record Contains the information from a cel file</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">The following classes are DEPRECATED:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">class CelParser: parses cel files</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">class CelRecord: stores the information from a cel file</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Affy.CelFile.Record-class.html">Record</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> Stores the information in a cel file</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.Record-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.intensities()=Bio.Affy.CelFile.CelRecord-class.html#intensities"><a title="Bio.Affy.CelFile.CelRecord.intensities" class="py-name" href="#" onclick="return doclink('link-0', 'intensities', 'link-0');">intensities</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.stdevs()=Bio.Affy.CelFile.CelRecord-class.html#stdevs"><a title="Bio.Affy.CelFile.CelRecord.stdevs" class="py-name" href="#" onclick="return doclink('link-1', 'stdevs', 'link-1');">stdevs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.npix()=Bio.Affy.CelFile.CelRecord-class.html#npix"><a title="Bio.Affy.CelFile.CelRecord.npix" class="py-name" href="#" onclick="return doclink('link-2', 'npix', 'link-2');">npix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.nrows()=Bio.Affy.CelFile.CelRecord-class.html#nrows"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-3', 'nrows', 'link-3');">nrows</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.ncols()=Bio.Affy.CelFile.CelRecord-class.html#ncols"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-4', 'ncols', 'link-4');">ncols</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="read"></a><div id="read-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="read-toggle" onclick="return toggle('read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile-module.html#read">read</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> Read the information in a cel file, and store it in a Record.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-comment"># Needs error handling.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-comment"># Needs to know the chip design.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name" targets="Class Bio.Affy.CelFile.Record=Bio.Affy.CelFile.Record-class.html,Module Bio.Blast.Record=Bio.Blast.Record-module.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Class Bio.Emboss.Primer3.Record=Bio.Emboss.Primer3.Record-class.html,Class Bio.ExPASy.Enzyme.Record=Bio.ExPASy.Enzyme.Record-class.html,Class Bio.ExPASy.Prodoc.Record=Bio.ExPASy.Prodoc.Record-class.html,Class Bio.ExPASy.Prosite.Record=Bio.ExPASy.Prosite.Record-class.html,Class Bio.ExPASy.ScanProsite.Record=Bio.ExPASy.ScanProsite.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Class Bio.Motif.Parsers.AlignAce.Record=Bio.Motif.Parsers.AlignAce.Record-class.html,Class Bio.Motif.Parsers.MAST.Record=Bio.Motif.Parsers.MAST.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.LargeFileParser.Record=Bio.PopGen.GenePop.LargeFileParser.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.Record=Bio.SwissProt.Record-class.html,Class Bio.UniGene.Record=Bio.UniGene.Record-class.html"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-5', 'Record', 'link-5');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-6" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-6', 'handle', 'link-6');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-7', 'strip', 'link-7');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"[HEADER]"</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">"HEADER"</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">11</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"[INTENSITY]"</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">"INTENSITY"</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.intensities" class="py-name" href="#" onclick="return doclink('link-8', 'intensities', 'link-0');">intensities</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-9', 'nrows', 'link-3');">nrows</a></tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-10', 'ncols', 'link-4');">ncols</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.stdevs" class="py-name" href="#" onclick="return doclink('link-11', 'stdevs', 'link-1');">stdevs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-12', 'nrows', 'link-3');">nrows</a></tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-13', 'ncols', 'link-4');">ncols</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.npix" class="py-name" href="#" onclick="return doclink('link-14', 'npix', 'link-2');">npix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-15', 'nrows', 'link-3');">nrows</a></tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-16', 'ncols', 'link-4');">ncols</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"["</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">section</tt><tt class="py-op">==</tt><tt class="py-string">"HEADER"</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">keyword</tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-17', 'value', 'link-17');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-18', 'split', 'link-18');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">keyword</tt><tt class="py-op">==</tt><tt class="py-string">"Cols"</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.ncols" class="py-name" href="#" onclick="return doclink('link-19', 'ncols', 'link-4');">ncols</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-20', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">keyword</tt><tt class="py-op">==</tt><tt class="py-string">"Rows"</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.nrows" class="py-name" href="#" onclick="return doclink('link-21', 'nrows', 'link-3');">nrows</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-22', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">section</tt><tt class="py-op">==</tt><tt class="py-string">"INTENSITY"</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">if</tt> <tt class="py-string">"="</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-23', 'split', 'link-18');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt id="link-24" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-24');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.intensities" class="py-name" href="#" onclick="return doclink('link-25', 'intensities', 'link-0');">intensities</a></tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.stdevs" class="py-name" href="#" onclick="return doclink('link-27', 'stdevs', 'link-1');">stdevs</a></tt><tt class="py-op">[</tt><tt id="link-28" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.npix" class="py-name" href="#" onclick="return doclink('link-29', 'npix', 'link-2');">npix</a></tt><tt class="py-op">[</tt><tt id="link-30" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-30', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </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-comment"># Everything below is considered deprecated</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-31" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-31', 'Bio', 'link-31');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-32', 'ParserSupport', 'link-32');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-33" class="py-name" targets="Class Bio.ParserSupport.AbstractConsumer=Bio.ParserSupport.AbstractConsumer-class.html"><a title="Bio.ParserSupport.AbstractConsumer" class="py-name" href="#" onclick="return doclink('link-33', 'AbstractConsumer', 'link-33');">AbstractConsumer</a></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="CelScanner"></a><div id="CelScanner-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="CelScanner-toggle" onclick="return toggle('CelScanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelScanner-class.html">CelScanner</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelScanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CelScanner-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-docstring">"""Scanner for Affymetrix CEL files (DEPRECATED)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> feed Feed data into the scanner.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> The scanner generates (and calls the consumer) the following</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> types of events:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> Rows - the number of rows on the microarray</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> Cols - the number of columns on the microarray</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> StartIntensity - generated when the section [INTENSITY] is found</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> ReadIntensity - one line in the section [INTENSITY]</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="CelScanner.__init__"></a><div id="CelScanner.__init__-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="CelScanner.__init__-toggle" onclick="return toggle('CelScanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelScanner-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelScanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelScanner.__init__-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-34" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-34', 'Bio', 'link-31');">Bio</a></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Affy.CelFile.CelScanner is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt id="link-35" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-35', 'Bio', 'link-31');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Class Bio.BiopythonDeprecationWarning=Bio.BiopythonDeprecationWarning-class.html"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-36', 'BiopythonDeprecationWarning', 'link-36');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="CelScanner.feed"></a><div id="CelScanner.feed-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="CelScanner.feed-toggle" onclick="return toggle('CelScanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelScanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelScanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelScanner.feed-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""scanner.feed(handle, consumer)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> Feed in a handle to a Cel file for scanning. handle is a file-like</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> object that contains the Cel file. consumer is a Consumer</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> object that will receive events as the report is scanned.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-37" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-37', 'handle', 'link-6');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-38', 'strip', 'link-7');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"["</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"[HEADER]"</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">"HEADER"</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">11</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"[INTENSITY]"</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">section</tt> <tt class="py-op">=</tt> <tt class="py-string">"INTENSITY"</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.StartIntensity()=Bio.Affy.CelFile.CelConsumer-class.html#StartIntensity"><a title="Bio.Affy.CelFile.CelConsumer.StartIntensity" class="py-name" href="#" onclick="return doclink('link-39', 'StartIntensity', 'link-39');">StartIntensity</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">section</tt><tt class="py-op">==</tt><tt class="py-string">"HEADER"</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">keyword</tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-40', 'value', 'link-17');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-41', 'split', 'link-18');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">keyword</tt><tt class="py-op">==</tt><tt class="py-string">"Cols"</tt><tt class="py-op">:</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.Cols()=Bio.Affy.CelFile.CelConsumer-class.html#Cols"><a title="Bio.Affy.CelFile.CelConsumer.Cols" class="py-name" href="#" onclick="return doclink('link-42', 'Cols', 'link-42');">Cols</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-43', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">keyword</tt><tt class="py-op">==</tt><tt class="py-string">"Rows"</tt><tt class="py-op">:</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.Rows()=Bio.Affy.CelFile.CelConsumer-class.html#Rows"><a title="Bio.Affy.CelFile.CelConsumer.Rows" class="py-name" href="#" onclick="return doclink('link-44', 'Rows', 'link-44');">Rows</a></tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-45', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">section</tt><tt class="py-op">==</tt><tt class="py-string">"INTENSITY"</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"="</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.ReadIntensity()=Bio.Affy.CelFile.CelConsumer-class.html#ReadIntensity"><a title="Bio.Affy.CelFile.CelConsumer.ReadIntensity" class="py-name" href="#" onclick="return doclink('link-46', 'ReadIntensity', 'link-46');">ReadIntensity</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="CelConsumer"></a><div id="CelConsumer-def"><a name="L129"></a><tt class="py-lineno">129</tt> <a class="py-toggle" href="#" id="CelConsumer-toggle" onclick="return toggle('CelConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html">CelConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CelConsumer-expanded"><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-docstring">"""Consumer for Affymetrix CEL files (DEPRECATED)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="CelConsumer.__init__"></a><div id="CelConsumer.__init__-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="CelConsumer.__init__-toggle" onclick="return toggle('CelConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelConsumer.__init__-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-47" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-47', 'Bio', 'link-31');">Bio</a></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Affy.CelFile.CelConsumer is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-48', 'Bio', 'link-31');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-49', 'BiopythonDeprecationWarning', 'link-36');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mean</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdev</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="CelConsumer.Cols"></a><div id="CelConsumer.Cols-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="CelConsumer.Cols-toggle" onclick="return toggle('CelConsumer.Cols');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html#Cols">Cols</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer.Cols-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelConsumer.Cols-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cols</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-50', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="CelConsumer.Rows"></a><div id="CelConsumer.Rows-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="CelConsumer.Rows-toggle" onclick="return toggle('CelConsumer.Rows');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html#Rows">Rows</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer.Rows-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelConsumer.Rows-expanded"><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_rows</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-51', 'value', 'link-17');">value</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="CelConsumer.StartIntensity"></a><div id="CelConsumer.StartIntensity-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="CelConsumer.StartIntensity-toggle" onclick="return toggle('CelConsumer.StartIntensity');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html#StartIntensity">StartIntensity</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer.StartIntensity-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelConsumer.StartIntensity-expanded"><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mean</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_rows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cols</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdev</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_rows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cols</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_rows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cols</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="CelConsumer.ReadIntensity"></a><div id="CelConsumer.ReadIntensity-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="CelConsumer.ReadIntensity-toggle" onclick="return toggle('CelConsumer.ReadIntensity');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelConsumer-class.html#ReadIntensity">ReadIntensity</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelConsumer.ReadIntensity-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelConsumer.ReadIntensity-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt id="link-52" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-52', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Graph.GraphData.mean()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#mean"><a title="Bio.Graphics.GenomeDiagram._Graph.GraphData.mean" class="py-name" href="#" onclick="return doclink('link-53', 'mean', 'link-53');">mean</a></tt><tt class="py-op">,</tt> <tt id="link-54" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Graph.GraphData.stdev()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#stdev"><a title="Bio.Graphics.GenomeDiagram._Graph.GraphData.stdev" class="py-name" href="#" onclick="return doclink('link-54', 'stdev', 'link-54');">stdev</a></tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.npix" class="py-name" href="#" onclick="return doclink('link-55', 'npix', 'link-2');">npix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-56', 'split', 'link-18');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-57', 'x', 'link-24');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-58', 'x', 'link-24');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mean</tt><tt class="py-op">[</tt><tt id="link-59" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-59', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Graph.GraphData.mean" class="py-name" href="#" onclick="return doclink('link-60', 'mean', 'link-53');">mean</a></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdev</tt><tt class="py-op">[</tt><tt id="link-61" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-61', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Graph.GraphData.stdev" class="py-name" href="#" onclick="return doclink('link-62', 'stdev', 'link-54');">stdev</a></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-24');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.npix" class="py-name" href="#" onclick="return doclink('link-64', 'npix', 'link-2');">npix</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="CelRecord"></a><div id="CelRecord-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="CelRecord-toggle" onclick="return toggle('CelRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html">CelRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CelRecord-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Stores the information in a cel file (DEPRECATED).</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> Needs error handling.</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> Needs to know the chip design.</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the Record class instead.</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="CelRecord.__init__"></a><div id="CelRecord.__init__-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="CelRecord.__init__-toggle" onclick="return toggle('CelRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.__init__-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> Pass the data attributes as a dictionary.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-65" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-65', 'Bio', 'link-31');">Bio</a></tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Affy.CelFile.CelRecord is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-66', 'Bio', 'link-31');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-67', 'BiopythonDeprecationWarning', 'link-36');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-68" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.SeqIO._index._IndexedSeqFileDict.copy()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-68', 'copy', 'link-68');">copy</a></tt> <tt class="py-keyword">import</tt> <tt class="py-name">deepcopy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">dcopy</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt> <tt class="py-op">=</tt> <tt class="py-name">dcopy</tt><tt class="py-op">(</tt><tt class="py-name">data_dict</tt><tt class="py-op">[</tt><tt class="py-string">'intensities'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdevs</tt> <tt class="py-op">=</tt> <tt class="py-name">dcopy</tt><tt class="py-op">(</tt><tt class="py-name">data_dict</tt><tt class="py-op">[</tt><tt class="py-string">'stdevs'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> <tt class="py-op">=</tt> <tt class="py-name">dcopy</tt><tt class="py-op">(</tt><tt class="py-name">data_dict</tt><tt class="py-op">[</tt><tt class="py-string">'npix'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_nrows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ncols</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
<a name="CelRecord.intensities"></a><div id="CelRecord.intensities-def"><a name="L193"></a><tt class="py-lineno">193</tt> <a class="py-toggle" href="#" id="CelRecord.intensities-toggle" onclick="return toggle('CelRecord.intensities');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#intensities">intensities</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.intensities-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.intensities-expanded"><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> Return a two dimensional array of probe cell intensities.</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 1 -> rows</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 2 -> columns</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt> </tt>
</div><a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="CelRecord.stdevs"></a><div id="CelRecord.stdevs-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="CelRecord.stdevs-toggle" onclick="return toggle('CelRecord.stdevs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#stdevs">stdevs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.stdevs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.stdevs-expanded"><a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"> Return a two dimensional array of probe cell standard deviations.</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 1 -> rows</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 2 -> columns</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdevs</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
<a name="CelRecord.npix"></a><div id="CelRecord.npix-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="CelRecord.npix-toggle" onclick="return toggle('CelRecord.npix');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#npix">npix</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.npix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.npix-expanded"><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> Return a two dimensional array of the number of pixels in a probe cell.</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 1 -> rows</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> Dimension 2 -> columns</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="CelRecord.nrows"></a><div id="CelRecord.nrows-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="CelRecord.nrows-toggle" onclick="return toggle('CelRecord.nrows');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#nrows">nrows</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.nrows-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.nrows-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> The number of rows of probe cells in an array.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_nrows</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="CelRecord.ncols"></a><div id="CelRecord.ncols-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="CelRecord.ncols-toggle" onclick="return toggle('CelRecord.ncols');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#ncols">ncols</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.ncols-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.ncols-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> The number of columns of probe cells in an array.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ncols</tt> </tt>
</div><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="CelRecord.size"></a><div id="CelRecord.size-def"><a name="L232"></a><tt class="py-lineno">232</tt> <a class="py-toggle" href="#" id="CelRecord.size-toggle" onclick="return toggle('CelRecord.size');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelRecord-class.html#size">size</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelRecord.size-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelRecord.size-expanded"><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> The size of the probe cell array as a tuple (nrows,ncols).</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_nrows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ncols</tt> </tt>
</div></div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="CelParser"></a><div id="CelParser-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="CelParser-toggle" onclick="return toggle('CelParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelParser-class.html">CelParser</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CelParser-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> Takes a handle to an Affymetrix cel file, parses the file and</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> returns an instance of a CelRecord</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> This class needs error handling.</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="CelParser.__init__"></a><div id="CelParser.__init__-def"><a name="L251"></a><tt class="py-lineno">251</tt> <a class="py-toggle" href="#" id="CelParser.__init__-toggle" onclick="return toggle('CelParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelParser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelParser.__init__-expanded"><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> Usually load the class with the cel file (not file name) as</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> an argument.</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-69" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-69', 'Bio', 'link-31');">Bio</a></tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Affy.CelFile.CelParser is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-70', 'Bio', 'link-31');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-71', 'BiopythonDeprecationWarning', 'link-36');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdevs</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-72" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-72', 'handle', 'link-6');">handle</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-73', 'parse', 'link-73');">parse</a></tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-74', 'handle', 'link-6');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="CelParser.parse"></a><div id="CelParser.parse-def"><a name="L268"></a><tt class="py-lineno">268</tt> <a class="py-toggle" href="#" id="CelParser.parse-toggle" onclick="return toggle('CelParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelParser.parse-expanded"><a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> Takes a handle to a cel file, parses it</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> and stores it in the three arrays.</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> There is more information in the cel file that could be retrieved</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-docstring"> and stored in CelRecord. The chip type should be a priority.</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-comment"># (self._intensities, self._stdevs, self._npix) = _cel.parse(data)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">scanner</tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name" targets="Class Bio.Affy.CelFile.CelScanner=Bio.Affy.CelFile.CelScanner-class.html"><a title="Bio.Affy.CelFile.CelScanner" class="py-name" href="#" onclick="return doclink('link-75', 'CelScanner', 'link-75');">CelScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">consumer</tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name" targets="Class Bio.Affy.CelFile.CelConsumer=Bio.Affy.CelFile.CelConsumer-class.html"><a title="Bio.Affy.CelFile.CelConsumer" class="py-name" href="#" onclick="return doclink('link-76', 'CelConsumer', 'link-76');">CelConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">scanner</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ExPASy.ScanProsite.Parser.feed()=Bio.ExPASy.ScanProsite.Parser-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.UniGene.UniGene.UniGeneParser.feed()=Bio.UniGene.UniGene.UniGeneParser-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ExPASy.ScanProsite.Parser.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.UniGene.UniGene.UniGeneParser.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-77', 'feed', 'link-77');">feed</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-78', 'handle', 'link-6');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt> <tt class="py-op">=</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">_mean</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdevs</tt> <tt class="py-op">=</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">_stdev</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> <tt class="py-op">=</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_nrows</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ncols</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="CelParser.__call__"></a><div id="CelParser.__call__-def"><a name="L288"></a><tt class="py-lineno">288</tt> <a class="py-toggle" href="#" id="CelParser.__call__-toggle" onclick="return toggle('CelParser.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Affy.CelFile.CelParser-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CelParser.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CelParser.__call__-expanded"><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> Returns the parsed data as a CelRecord.</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">record_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">record_dict</tt><tt class="py-op">[</tt><tt class="py-string">'intensities'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_intensities</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">record_dict</tt><tt class="py-op">[</tt><tt class="py-string">'stdevs'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stdevs</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">record_dict</tt><tt class="py-op">[</tt><tt class="py-string">'npix'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_npix</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-79" class="py-name" targets="Class Bio.Affy.CelFile.CelRecord=Bio.Affy.CelFile.CelRecord-class.html"><a title="Bio.Affy.CelFile.CelRecord" class="py-name" href="#" onclick="return doclink('link-79', 'CelRecord', 'link-79');">CelRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">record_dict</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> </tt><script type="text/javascript">
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