208 lines
22 KiB
HTML
208 lines
22 KiB
HTML
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<a href="obitools-module.html">Package obitools</a> ::
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Package options
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<h1 class="epydoc">Source Code for <a href="obitools.options-module.html">Package obitools.options</a></h1>
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<pre class="py-src">
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<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
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<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"> Module providing high level functions to manage command line options.</tt> </tt>
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<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">logging</tt> </tt>
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<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
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<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
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<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">logging</tt> <tt class="py-keyword">import</tt> <tt class="py-name">debug</tt> </tt>
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<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
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<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">optparse</tt> <tt class="py-keyword">import</tt> <tt class="py-name">OptionParser</tt> </tt>
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<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
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<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-1', 'utils', 'link-1');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function obitools.utils.universalOpen()=obitools.utils-module.html#universalOpen"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-2', 'universalOpen', 'link-2');">universalOpen</a></tt> </tt>
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<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
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<a name="getOptionManager"></a><div id="getOptionManager-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="getOptionManager-toggle" onclick="return toggle('getOptionManager');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.options-module.html#getOptionManager">getOptionManager</a><tt class="py-op">(</tt><tt class="py-param">optionDefinitions</tt><tt class="py-op">,</tt><tt class="py-param">entryIterator</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="getOptionManager-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="getOptionManager-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring"> Build an option manager fonction. that is able to parse</tt> </tt>
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<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> command line options of the script.</tt> </tt>
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<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> @param optionDefinitions: list of function describing a set of </tt> </tt>
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<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> options. Each function must allows as</tt> </tt>
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<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> unique parametter an instance of OptionParser.</tt> </tt>
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<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> @type optionDefinitions: list of functions.</tt> </tt>
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<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> @param entryIterator: an iterator generator function returning</tt> </tt>
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<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> entries from the data files. </tt> </tt>
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<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> @type entryIterator: an iterator generator function with only one</tt> </tt>
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<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> parametter of type file</tt> </tt>
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<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Module obitools.obo.parser=obitools.obo.parser-module.html,Module obitools.seqdb.genbank.parser=obitools.seqdb.genbank.parser-module.html"><a title="obitools.obo.parser
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obitools.seqdb.genbank.parser" class="py-name" href="#" onclick="return doclink('link-3', 'parser', 'link-3');">parser</a></tt> <tt class="py-op">=</tt> <tt class="py-name">OptionParser</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="obitools.obo.parser
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obitools.seqdb.genbank.parser" class="py-name" href="#" onclick="return doclink('link-4', 'parser', 'link-3');">parser</a></tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-D'</tt><tt class="py-op">,</tt><tt class="py-string">'--DEBUG'</tt><tt class="py-op">,</tt> </tt>
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<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store_true"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"debug"</tt><tt class="py-op">,</tt> </tt>
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<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
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<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Set logging in debug mode"</tt><tt class="py-op">)</tt> </tt>
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<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt>
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<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> </tt>
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<a name="L36"></a><tt class="py-lineno">36</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">optionDefinitions</tt><tt class="py-op">:</tt> </tt>
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<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="obitools.obo.parser
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obitools.seqdb.genbank.parser" class="py-name" href="#" onclick="return doclink('link-5', 'parser', 'link-3');">parser</a></tt><tt class="py-op">)</tt> </tt>
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<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt>
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<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">commandLineAnalyzer</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt id="link-6" class="py-name" targets="Module obitools.obischemas.options=obitools.obischemas.options-module.html,Package obitools.options=obitools.options-module.html,Module obitools.word.options=obitools.word.options-module.html"><a title="obitools.obischemas.options
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obitools.options
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obitools.word.options" class="py-name" href="#" onclick="return doclink('link-6', 'options', 'link-6');">options</a></tt><tt class="py-op">,</tt><tt class="py-name">files</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="obitools.obo.parser
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obitools.seqdb.genbank.parser" class="py-name" href="#" onclick="return doclink('link-7', 'parser', 'link-3');">parser</a></tt><tt class="py-op">.</tt><tt class="py-name">parse_args</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
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<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-8" class="py-name"><a title="obitools.obischemas.options
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obitools.options
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obitools.word.options" class="py-name" href="#" onclick="return doclink('link-8', 'options', 'link-6');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">debug</tt><tt class="py-op">:</tt> </tt>
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<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt class="py-name">setLevel</tt><tt class="py-op">(</tt><tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">DEBUG</tt><tt class="py-op">)</tt> </tt>
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<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
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<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Function obitools.options.allEntryIterator()=obitools.options-module.html#allEntryIterator"><a title="obitools.options.allEntryIterator" class="py-name" href="#" onclick="return doclink('link-9', 'allEntryIterator', 'link-9');">allEntryIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">files</tt><tt class="py-op">,</tt><tt class="py-name">entryIterator</tt><tt class="py-op">)</tt> </tt>
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<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="obitools.obischemas.options
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obitools.options
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obitools.word.options" class="py-name" href="#" onclick="return doclink('link-10', 'options', 'link-6');">options</a></tt><tt class="py-op">,</tt><tt class="py-name">i</tt> </tt>
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</div><a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> </tt>
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<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">commandLineAnalyzer</tt> </tt>
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</div><a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> </tt>
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<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Variable obitools.options._currentInputFileName=obitools.options-module.html#_currentInputFileName"><a title="obitools.options._currentInputFileName" class="py-name" href="#" onclick="return doclink('link-11', '_currentInputFileName', 'link-11');">_currentInputFileName</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
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<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> </tt>
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<a name="currentInputFileName"></a><div id="currentInputFileName-def"><a name="L52"></a><tt class="py-lineno">52</tt> <a class="py-toggle" href="#" id="currentInputFileName-toggle" onclick="return toggle('currentInputFileName');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.options-module.html#currentInputFileName">currentInputFileName</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="currentInputFileName-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="currentInputFileName-expanded"><a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-12" class="py-name"><a title="obitools.options._currentInputFileName" class="py-name" href="#" onclick="return doclink('link-12', '_currentInputFileName', 'link-11');">_currentInputFileName</a></tt> </tt>
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</div><a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> </tt>
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<a name="allEntryIterator"></a><div id="allEntryIterator-def"><a name="L55"></a><tt class="py-lineno">55</tt> <a class="py-toggle" href="#" id="allEntryIterator-toggle" onclick="return toggle('allEntryIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.options-module.html#allEntryIterator">allEntryIterator</a><tt class="py-op">(</tt><tt class="py-param">files</tt><tt class="py-op">,</tt><tt class="py-param">entryIterator</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="allEntryIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="allEntryIterator-expanded"><a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt id="link-13" class="py-name"><a title="obitools.options._currentInputFileName" class="py-name" href="#" onclick="return doclink('link-13', '_currentInputFileName', 'link-11');">_currentInputFileName</a></tt> </tt>
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<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">files</tt> <tt class="py-op">:</tt> </tt>
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<a name="L58"></a><tt class="py-lineno">58</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">files</tt><tt class="py-op">:</tt> </tt>
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<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="obitools.options._currentInputFileName" class="py-name" href="#" onclick="return doclink('link-14', '_currentInputFileName', 'link-11');">_currentInputFileName</a></tt><tt class="py-op">=</tt><tt class="py-name">f</tt> </tt>
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<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-15', 'universalOpen', 'link-2');">universalOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
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<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-name">debug</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
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<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">entryIterator</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
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<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">f</tt><tt class="py-op">:</tt> </tt>
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<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">line</tt> </tt>
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<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
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<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entryIterator</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">entry</tt> </tt>
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<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
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<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">entryIterator</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
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<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt><tt class="py-op">:</tt> </tt>
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<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">line</tt> </tt>
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<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
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