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Collect_SILAC_XML-pysrc.html
Collect_SILAC_XML-pysrc.html 78.60 KiB
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Module Collect_SILAC_XML
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<h1 class="epydoc">Source Code for <a href="Collect_SILAC_XML-module.html">Module Collect_SILAC_XML</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">Collect_SILAC_XML.py</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">Allow collection of SILAC XML file results after</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">validation, calculates statistics and generates</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">a table with results, aggregating the results</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">for each protein (as an option)</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">Usage: python Collect_SILAC_XML.py -f <folder with XML SILAC files> -s</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">(switch to obtain the output in aggregated or summary form)</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">Output is to stdout</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">First argument - folder with XML files</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">Output - table in tab delimited format containing</tt> </tt><a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">the statistics for each validated protein, printed to stdout</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">This script is provided "as is" and works well with correctly</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">formatted XML SILAC files. However, no exceptions have been</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">implemented and the code will fail if not fed correct data</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 class="py-docstring">Cosmin Saveanu, last modifications 2008-04-14</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Genetique des Interactions Macromoleculaires, </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">Alain Jacquier's lab, Institut Pasteur,</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">CNRS-URA 2171, France</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">csaveanu@pasteur.fr for any questions</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>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment">#import cElementTree as ET (for versions of Python < 2.5)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">etree</tt><tt class="py-op">.</tt><tt class="py-name">cElementTree</tt> <tt class="py-keyword">as</tt> <tt class="py-name">ET</tt> <tt class="py-comment">#latest version integrated in Python 2.5</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">math</tt><tt class="py-op">,</tt> <tt class="py-name">getopt</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment">#a dictionary that holds the position of the different</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#informations available in the SILAC XML file</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#used by GetValXML</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-0" class="py-name" targets="Variable Collect_SILAC_XML.XMLdict=Collect_SILAC_XML-module.html#XMLdict"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-0', 'XMLdict', 'link-0');">XMLdict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">:</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">'ratio'</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">'local_bg'</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">:</tt><tt class="py-number">9</tt><tt class="py-op">}</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt>
<a name="Mean"></a><div id="Mean-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="Mean-toggle" onclick="return toggle('Mean');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Mean">Mean</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Mean-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Mean-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the mean of the values from a list</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> Returns 0 if the list is empty</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</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">sum</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sum</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="SumSquares"></a><div id="SumSquares-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="SumSquares-toggle" onclick="return toggle('SumSquares');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#SumSquares">SumSquares</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SumSquares-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SumSquares-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> Squares each value in the passed list, adds up these squares and</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> returns the result.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">ss</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</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">ss</tt> <tt class="py-op">=</tt> <tt class="py-name">ss</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt><tt class="py-op">*</tt><tt class="py-name">item</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ss</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="Variance"></a><div id="Variance-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="Variance-toggle" onclick="return toggle('Variance');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Variance">Variance</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Variance-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Variance-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the variance for a sample </tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> Returns 100 if less than 2 values are provided</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name" targets="Function Collect_SILAC_XML.Mean()=Collect_SILAC_XML-module.html#Mean,Function lilamsxml.Mean()=lilamsxml-module.html#Mean"><a title="Collect_SILAC_XML.Mean
lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-1', 'Mean', 'link-1');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">ssq</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name" targets="Function Collect_SILAC_XML.SumSquares()=Collect_SILAC_XML-module.html#SumSquares,Function lilamsxml.SumSquares()=lilamsxml-module.html#SumSquares"><a title="Collect_SILAC_XML.SumSquares
lilamsxml.SumSquares" class="py-name" href="#" onclick="return doclink('link-2', 'SumSquares', 'link-2');">SumSquares</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </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">n</tt> <tt class="py-op">></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ssq</tt> <tt class="py-op">-</tt> <tt class="py-name">n</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">vari</tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="StdDev"></a><div id="StdDev-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="StdDev-toggle" onclick="return toggle('StdDev');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#StdDev">StdDev</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StdDev-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StdDev-expanded"><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"> Returns the standard deviation of the values in the passed list</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> using N-1 in the denominator (i.e., to estimate population stdev).</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"> """</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name" targets="Function Collect_SILAC_XML.Variance()=Collect_SILAC_XML-module.html#Variance,Function lilamsxml.Variance()=lilamsxml-module.html#Variance"><a title="Collect_SILAC_XML.Variance
lilamsxml.Variance" class="py-name" href="#" onclick="return doclink('link-3', 'Variance', 'link-3');">Variance</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="Median"></a><div id="Median-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="Median-toggle" onclick="return toggle('Median');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Median">Median</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Median-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Median-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> Returns the median of the passed list.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> Returns 0 or the element if less than 2 elements</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> are passed to the function</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">newlist</tt> <tt class="py-op">=</tt> <tt class="py-name">inlist</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">newlist</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</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-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># if even number, simple mean of middles</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">median</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="get_flist"></a><div id="get_flist-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="get_flist-toggle" onclick="return toggle('get_flist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#get_flist">get_flist</a><tt class="py-op">(</tt><tt class="py-param">dirname</tt><tt class="py-op">,</tt> <tt class="py-param">ext</tt> <tt class="py-op">=</tt> <tt class="py-string">".xml"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_flist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_flist-expanded"><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> Get all .ext file names from dirname, not recursive</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> returns list of complete paths for files</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">dirname</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-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">f</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">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment">#we do nothing with the subfolders</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">extension</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">ext</tt><tt class="py-op">,</tt><tt class="py-op">)</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">outlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outlist</tt> </tt>
</div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="GetValXML"></a><div id="GetValXML-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="GetValXML-toggle" onclick="return toggle('GetValXML');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#GetValXML">GetValXML</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">=</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GetValXML-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetValXML-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> Returns the text attribute of an entry in an ElementTree</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> object based on the XMLdict dictionary that maps</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> numbers to tags - definition in the init of the main</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> frame. By default it returns the peptide sequence of </tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> the first record.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> pdatapos - indicates the position of the <pepdata> in</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> the root of the pepdata xml entry</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">pdatapos</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-4" class="py-name"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-4', 'XMLdict', 'link-0');">XMLdict</a></tt><tt class="py-op">[</tt><tt class="py-name">what</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="GenerateListDict"></a><div id="GenerateListDict-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="GenerateListDict-toggle" onclick="return toggle('GenerateListDict');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#GenerateListDict">GenerateListDict</a><tt class="py-op">(</tt><tt class="py-param">xmldata</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenerateListDict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenerateListDict-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> Recovers the data about a peptide in the XML SILAC file</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Returns a dictionary, each peptide has an integer as key</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">entriesdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">entriesdict</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-5" class="py-name" targets="Function Collect_SILAC_XML.GetValXML()=Collect_SILAC_XML-module.html#GetValXML,Method silacvalidator.MainFrame.GetValXML()=silacvalidator.MainFrame-class.html#GetValXML"><a title="Collect_SILAC_XML.GetValXMLsilacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-5', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'pepseq'</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 id="link-6" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-6', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</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 id="link-7" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-7', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-8', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-9', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-10', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</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-11" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-11', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-12', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-13', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'local_bg'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Collect_SILAC_XML.GetValXML
silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-14', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">entriesdict</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="CalcStatistics"></a><div id="CalcStatistics-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="CalcStatistics-toggle" onclick="return toggle('CalcStatistics');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#CalcStatistics">CalcStatistics</a><tt class="py-op">(</tt><tt class="py-param">datadict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CalcStatistics-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CalcStatistics-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"> Returns statistics on a single data dictionary (corresponding to one protein)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> as a multiple of strings <nr of valid peptides>, <median>, <mean>, <SD></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">yeslist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">yeskeylist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">datadict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">yeskeylist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">yeslist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment">#7 is calculated corrected ratio index</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Function Collect_SILAC_XML.Median()=Collect_SILAC_XML-module.html#Median,Function lilamsxml.Median()=lilamsxml-module.html#Median"><a title="Collect_SILAC_XML.Median
lilamsxml.Median" class="py-name" href="#" onclick="return doclink('link-15', 'Median', 'link-15');">Median</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">mean</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Collect_SILAC_XML.Mean
lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-16', 'Mean', 'link-1');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">stddev</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Function Collect_SILAC_XML.StdDev()=Collect_SILAC_XML-module.html#StdDev,Function lilamsxml.StdDev()=lilamsxml-module.html#StdDev"><a title="Collect_SILAC_XML.StdDev
lilamsxml.StdDev" class="py-name" href="#" onclick="return doclink('link-17', 'StdDev', 'link-17');">StdDev</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">nopep</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-string">"%d"</tt><tt class="py-op">%</tt><tt class="py-name">nopep</tt><tt class="py-op">,</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-name">median</tt><tt class="py-op">,</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-name">mean</tt><tt class="py-op">,</tt> <tt class="py-string">"%.4f"</tt><tt class="py-op">%</tt><tt class="py-name">stddev</tt><tt class="py-op">)</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="ExtractSILACDataFromXML"></a><div id="ExtractSILACDataFromXML-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="ExtractSILACDataFromXML-toggle" onclick="return toggle('ExtractSILACDataFromXML');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#ExtractSILACDataFromXML">ExtractSILACDataFromXML</a><tt class="py-op">(</tt><tt class="py-param">fname</tt><tt class="py-op">,</tt> <tt class="py-param">peptides_also</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExtractSILACDataFromXML-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExtractSILACDataFromXML-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses an XML Silac file and returns information</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> on all the validated peptides in the entry if peptides_also</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> is True. The origin of the peptide (protein) is</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> also recovered and used in the output. Uses:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> - GenerateListDict - to obtain the peptide data</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> - CalcStatistics - to calculate protein SILAC statistics. </tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> Returns a string, formatted differently if peptides_also</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> is true or false</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">tree</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">parse</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">getroot</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">fsplit</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">endofname</tt> <tt class="py-op">=</tt> <tt class="py-name">fsplit</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment">#the root is a <protdata> entry</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">prot_data</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">endofname</tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">data</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-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">data</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-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">data</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-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">data</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-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">data</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-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">data</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-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment">#print "> Mowse score: %s, database: %s, ppm tolerance: %s"%(data[0][3].text,</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># data[0][1].text, data[0][2].text)</tt> </tt><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Spot identification: %s.\n"%data[0][0].text</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Identified protein: %s, accesion number: %s."%(data[2].text, data[1].text)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Peptide coverage: %s percent, matched peptides: %s."%(data[0][4].text[:-1], data[0][5].text)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">datadict</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name" targets="Function Collect_SILAC_XML.GenerateListDict()=Collect_SILAC_XML-module.html#GenerateListDict,Method silacvalidator.MainFrame.GenerateListDict()=silacvalidator.MainFrame-class.html#GenerateListDict"><a title="Collect_SILAC_XML.GenerateListDict
silacvalidator.MainFrame.GenerateListDict" class="py-name" href="#" onclick="return doclink('link-18', 'GenerateListDict', 'link-18');">GenerateListDict</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">stats</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Function Collect_SILAC_XML.CalcStatistics()=Collect_SILAC_XML-module.html#CalcStatistics"><a title="Collect_SILAC_XML.CalcStatistics" class="py-name" href="#" onclick="return doclink('link-19', 'CalcStatistics', 'link-19');">CalcStatistics</a></tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">stats_string</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">peptides_also</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">peptide_info_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">peptkey</tt> <tt class="py-keyword">in</tt> <tt class="py-name">datadict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">peptkey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">peptide_info_list</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">prot_data</tt><tt class="py-op">,</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">peptkey</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">stats_string</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">peptide_info_list</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">prot_data</tt><tt class="py-op">,</tt> <tt class="py-name">stats_string</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="Usage"></a><div id="Usage-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="Usage-toggle" onclick="return toggle('Usage');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Collect_SILAC_XML.Usage-class.html">Usage</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Usage-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Usage-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"> used for catching exceptions generated</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> during command line parameter parsing</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Usage.__init__"></a><div id="Usage.__init__-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="Usage.__init__-toggle" onclick="return toggle('Usage.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML.Usage-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">msg</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Usage.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Usage.__init__-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable silacvalidator.msg=silacvalidator-module.html#msg"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-20', 'msg', 'link-20');">msg</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-21', 'msg', 'link-20');">msg</a></tt> </tt>
</div></div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-param">argv</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="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt class="py-name">foldername</tt><tt class="py-op">,</tt> <tt class="py-name">aggregate</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">argv</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">argv</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">opts</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">getopt</tt><tt class="py-op">(</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"hsf:"</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"help"</tt><tt class="py-op">,</tt> <tt class="py-string">"summary"</tt><tt class="py-op">,</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-string">"XMLfolder="</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">error</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-22', 'msg', 'link-20');">msg</a></tt><tt class="py-op">:</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-23" class="py-name" targets="Class Collect_SILAC_XML.Usage=Collect_SILAC_XML.Usage-class.html,Class lilamsxml.Usage=lilamsxml.Usage-class.html"><a title="Collect_SILAC_XML.Usage
lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-23', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-24', 'msg', 'link-20');">msg</a></tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-comment"># option processing</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">foldername</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">aggregate</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">option</tt><tt class="py-op">,</tt> <tt class="py-name">value</tt> <tt class="py-keyword">in</tt> <tt class="py-name">opts</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-h"</tt><tt class="py-op">,</tt> <tt class="py-string">"--help"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-25" class="py-name"><a title="Collect_SILAC_XML.Usage
lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-25', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-name">__doc__</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-s"</tt><tt class="py-op">,</tt> <tt class="py-string">"--summary"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">aggregate</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-f"</tt><tt class="py-op">,</tt> <tt class="py-string">"--XMLfolder"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">foldername</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</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-op">(</tt><tt class="py-name">foldername</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-26" class="py-name"><a title="Collect_SILAC_XML.Usage
lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-26', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-string">"no input folder!"</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">flist</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Function Collect_SILAC_XML.get_flist()=Collect_SILAC_XML-module.html#get_flist"><a title="Collect_SILAC_XML.get_flist" class="py-name" href="#" onclick="return doclink('link-27', 'get_flist', 'link-27');">get_flist</a></tt><tt class="py-op">(</tt><tt class="py-name">foldername</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">header_identif</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"file_name"</tt><tt class="py-op">,</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-string">"Mowse_score"</tt><tt class="py-op">,</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-string">"Database"</tt><tt class="py-op">,</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-string">"ppm_tolerance"</tt><tt class="py-op">,</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-string">"Spot_identification"</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-string">"Identified_protein"</tt><tt class="py-op">,</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-string">"Accesion_number"</tt><tt class="py-op">,</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-string">"Peptide_coverage"</tt><tt class="py-op">,</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-string">"%_matched_peptides"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">header_stats</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"Number_of_valid_peptides"</tt><tt class="py-op">,</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-string">"Median_ratio"</tt><tt class="py-op">,</tt> <tt class="py-string">"Mean_ratio"</tt><tt class="py-op">,</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-string">"Std_Dev"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">aggregate</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">header_pep</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">,</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-string">'leucines'</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-string">'mzh'</tt><tt class="py-op">,</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">'ratio'</tt><tt class="py-op">,</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">,</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-string">'local_bg'</tt><tt class="py-op">,</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-string">'validated'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">header_identif</tt><tt class="py-op">,</tt> <tt class="py-name">header_pep</tt><tt class="py-op">,</tt> <tt class="py-name">header_stats</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">header_identif</tt><tt class="py-op">,</tt> <tt class="py-name">header_stats</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">header</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">fname</tt> <tt class="py-keyword">in</tt> <tt class="py-name">flist</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-28" class="py-name" targets="Function Collect_SILAC_XML.ExtractSILACDataFromXML()=Collect_SILAC_XML-module.html#ExtractSILACDataFromXML"><a title="Collect_SILAC_XML.ExtractSILACDataFromXML" class="py-name" href="#" onclick="return doclink('link-28', 'ExtractSILACDataFromXML', 'link-28');">ExtractSILACDataFromXML</a></tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt> <tt class="py-name">peptides_also</tt><tt class="py-op">=</tt> <tt class="py-keyword">not</tt> <tt class="py-name">aggregate</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-29" class="py-name"><a title="Collect_SILAC_XML.Usage
lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-29', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</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-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">": "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-30', 'msg', 'link-20');">msg</a></tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-string">"\t for help use --help or -h"</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">2</tt> </tt>
</div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt id="link-31" class="py-name" targets="Function Collect_SILAC_XML.main()=Collect_SILAC_XML-module.html#main,Function lilamsxml.main()=lilamsxml-module.html#main"><a title="Collect_SILAC_XML.main
lilamsxml.main" class="py-name" href="#" onclick="return doclink('link-31', 'main', 'link-31');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt><script type="text/javascript">
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