1554 lines
237 KiB
HTML
1554 lines
237 KiB
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<h1 class="epydoc">Source Code for <a href="obitools.obo.parser-module.html">Module obitools.obo.parser</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-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.skipWhiteLineIterator()=obitools.utils-module.html#skipWhiteLineIterator"><a title="obitools.utils.skipWhiteLineIterator" class="py-name" href="#" onclick="return doclink('link-2', 'skipWhiteLineIterator', 'link-2');">skipWhiteLineIterator</a></tt><tt class="py-op">,</tt><tt id="link-3" class="py-name" targets="Function obitools.utils.multiLineWrapper()=obitools.utils-module.html#multiLineWrapper"><a title="obitools.utils.multiLineWrapper" class="py-name" href="#" onclick="return doclink('link-3', 'multiLineWrapper', 'link-3');">multiLineWrapper</a></tt> </tt>
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<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-5', 'utils', 'link-1');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" 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-6', 'universalOpen', 'link-6');">universalOpen</a></tt> </tt>
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<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-7', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Package obitools.format=obitools.format-module.html"><a title="obitools.format" class="py-name" href="#" onclick="return doclink('link-8', 'format', 'link-8');">format</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Package obitools.format.genericparser=obitools.format.genericparser-module.html"><a title="obitools.format.genericparser" class="py-name" href="#" onclick="return doclink('link-9', 'genericparser', 'link-9');">genericparser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Function obitools.format.genericparser.genericEntryIteratorGenerator()=obitools.format.genericparser-module.html#genericEntryIteratorGenerator"><a title="obitools.format.genericparser.genericEntryIteratorGenerator" class="py-name" href="#" onclick="return doclink('link-10', 'genericEntryIteratorGenerator', 'link-10');">genericEntryIteratorGenerator</a></tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</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 class="py-op">,</tt><tt class="py-name">warning</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">re</tt> </tt>
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<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </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-comment">#################################################################################</tt> </tt>
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<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## Stanza preparation area ##</tt> </tt>
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<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
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<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
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<a name="FileFormatError"></a><div id="FileFormatError-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="FileFormatError-toggle" onclick="return toggle('FileFormatError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.FileFormatError-class.html">FileFormatError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="FileFormatError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FileFormatError-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> An error derived from the class Exception.</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-keyword">pass</tt> </tt>
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</div><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
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<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-name">_oboEntryIterator</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="obitools.format.genericparser.genericEntryIteratorGenerator" class="py-name" href="#" onclick="return doclink('link-11', 'genericEntryIteratorGenerator', 'link-10');">genericEntryIteratorGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">endEntry</tt><tt class="py-op">=</tt><tt class="py-string">'^ *$'</tt><tt class="py-op">,</tt> </tt>
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<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">strip</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
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<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
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<a name="stanzaIterator"></a><div id="stanzaIterator-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="stanzaIterator-toggle" onclick="return toggle('stanzaIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#stanzaIterator">stanzaIterator</a><tt class="py-op">(</tt><tt class="py-param">inputfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="stanzaIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="stanzaIterator-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> Iterator of stanza. The stanza are the basic units of OBO files.</tt> </tt>
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<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> @param inputfile: a stream of strings from an opened OBO 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"> @type inputfile: a stream of strings</tt> </tt>
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<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> @return: a stream of stanza</tt> </tt>
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<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: a stream of aggregated strings</tt> </tt>
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<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> @note: The iterator constructs stanza by aggregate strings from the</tt> </tt>
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<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> OBO file.</tt> </tt>
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<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">inputfile</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-12', 'universalOpen', 'link-6');">universalOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">inputfile</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">inputfile</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="obitools.utils.multiLineWrapper" class="py-name" href="#" onclick="return doclink('link-13', 'multiLineWrapper', 'link-3');">multiLineWrapper</a></tt><tt class="py-op">(</tt><tt class="py-name">inputfile</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 class="py-keyword">return</tt> <tt class="py-name">_oboEntryIterator</tt><tt class="py-op">(</tt><tt class="py-name">inputfile</tt><tt class="py-op">)</tt> </tt>
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</div><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
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<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </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-comment">#################################################################################</tt> </tt>
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<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## Trailing Modifiers treatment area ##</tt> </tt>
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<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
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<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
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<a name="TrailingModifier"></a><div id="TrailingModifier-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="TrailingModifier-toggle" onclick="return toggle('TrailingModifier');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.TrailingModifier-class.html">TrailingModifier</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TrailingModifier-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TrailingModifier-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> A class object which inherits from the class dict. Trailing modifiers can be found</tt> </tt>
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<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> at the end of TaggedValue objects when they exist.</tt> </tt>
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<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
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<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt id="link-14" class="py-name" targets="Variable obitools.obo.parser.TrailingModifier._match_brace=obitools.obo.parser.TrailingModifier-class.html#_match_brace"><a title="obitools.obo.parser.TrailingModifier._match_brace" class="py-name" href="#" onclick="return doclink('link-14', '_match_brace', 'link-14');">_match_brace</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'(?<=\ {)[^\]]*(\}) *( !|$)'</tt><tt class="py-op">)</tt> </tt>
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<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
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<a name="TrailingModifier.__init__"></a><div id="TrailingModifier.__init__-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="TrailingModifier.__init__-toggle" onclick="return toggle('TrailingModifier.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.TrailingModifier-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">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TrailingModifier.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TrailingModifier.__init__-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
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<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment">## search for trailing modifiers signals</tt> </tt>
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<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">trailing_modifiers</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Class obitools.obo.parser.TrailingModifier=obitools.obo.parser.TrailingModifier-class.html"><a title="obitools.obo.parser.TrailingModifier" class="py-name" href="#" onclick="return doclink('link-15', 'TrailingModifier', 'link-15');">TrailingModifier</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="obitools.obo.parser.TrailingModifier._match_brace" class="py-name" href="#" onclick="return doclink('link-16', '_match_brace', 'link-14');">_match_brace</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">string</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>
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<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-comment">## the trailing modifiers exist</tt> </tt>
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<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">trailing_modifiers</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-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">.</tt><tt class="py-name">group</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">strip</tt><tt class="py-op">(</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">print</tt> <tt class="py-name">trailing_modifiers</tt> </tt>
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<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment">## creates and feeds the dictionary of trailing modifiers</tt> </tt>
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<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method obitools.BioSequence.__init__()=obitools.BioSequence-class.html#__init__,Method obitools.WrappedBioSequence.__init__()=obitools.WrappedBioSequence-class.html#__init__,Method obitools.WrapperSetIterator.__init__()=obitools.WrapperSetIterator-class.html#__init__,Method obitools.align.ssearch.SsearchParser.__init__()=obitools.align.ssearch.SsearchParser-class.html#__init__,Method obitools.blast.Blast.__init__()=obitools.blast.Blast-class.html#__init__,Method obitools.blast.BlastCovMinFilter.__init__()=obitools.blast.BlastCovMinFilter-class.html#__init__,Method obitools.blast.BlastResultIterator.__init__()=obitools.blast.BlastResultIterator-class.html#__init__,Method obitools.blast.NetBlast.__init__()=obitools.blast.NetBlast-class.html#__init__,Method obitools.cns.quality.QualitySequence.__init__()=obitools.cns.quality.QualitySequence-class.html#__init__,Method obitools.distances.DistanceMatrix.__init__()=obitools.distances.DistanceMatrix-class.html#__init__,Method obitools.ecopcr.EcoPCRFile.__init__()=obitools.ecopcr.EcoPCRFile-class.html#__init__,Method obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__()=obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html#__init__,Method obitools.ecopcr.taxonomy.Taxonomy.__init__()=obitools.ecopcr.taxonomy.Taxonomy-class.html#__init__,Method obitools.eutils.EFetch.__init__()=obitools.eutils.EFetch-class.html#__init__,Method obitools.eutils.EUtils.__init__()=obitools.eutils.EUtils-class.html#__init__,Method obitools.fast.Fast.__init__()=obitools.fast.Fast-class.html#__init__,Method obitools.format.genericparser.GenericParser.__init__()=obitools.format.genericparser.GenericParser-class.html#__init__,Method obitools.graph.DiGraph.__init__()=obitools.graph.DiGraph-class.html#__init__,Method obitools.graph.Edge.__init__()=obitools.graph.Edge-class.html#__init__,Method obitools.graph.Graph.__init__()=obitools.graph.Graph-class.html#__init__,Method obitools.graph.Indexer.__init__()=obitools.graph.Indexer-class.html#__init__,Method obitools.graph.Node.__init__()=obitools.graph.Node-class.html#__init__,Method obitools.graph.UndirectedGraph.__init__()=obitools.graph.UndirectedGraph-class.html#__init__,Method obitools.graph.dag.DAG.__init__()=obitools.graph.dag.DAG-class.html#__init__,Method obitools.gzip.GzipFile.__init__()=obitools.gzip.GzipFile-class.html#__init__,Method obitools.location.ComplementLocation.__init__()=obitools.location.ComplementLocation-class.html#__init__,Method obitools.location.CompositeLocation.__init__()=obitools.location.CompositeLocation-class.html#__init__,Method obitools.location.PointLocation.__init__()=obitools.location.PointLocation-class.html#__init__,Method obitools.location.SimpleLocation.__init__()=obitools.location.SimpleLocation-class.html#__init__,Method obitools.location.feature.Feature.__init__()=obitools.location.feature.Feature-class.html#__init__,Method obitools.obo.parser.DefValue.__init__()=obitools.obo.parser.DefValue-class.html#__init__,Method obitools.obo.parser.NameValue.__init__()=obitools.obo.parser.NameValue-class.html#__init__,Method obitools.obo.parser.NamespaceValue.__init__()=obitools.obo.parser.NamespaceValue-class.html#__init__,Method obitools.obo.parser.OBOEntry.__init__()=obitools.obo.parser.OBOEntry-class.html#__init__,Method obitools.obo.parser.OBOTerm.__init__()=obitools.obo.parser.OBOTerm-class.html#__init__,Method obitools.obo.parser.RelationshipValue.__init__()=obitools.obo.parser.RelationshipValue-class.html#__init__,Method obitools.obo.parser.RemarkValue.__init__()=obitools.obo.parser.RemarkValue-class.html#__init__,Method obitools.obo.parser.SynonymValue.__init__()=obitools.obo.parser.SynonymValue-class.html#__init__,Method obitools.obo.parser.TaggedValue.__init__()=obitools.obo.parser.TaggedValue-class.html#__init__,Method obitools.obo.parser.TrailingModifier.__init__()=obitools.obo.parser.TrailingModifier-class.html#__init__,Method obitools.obo.parser.Xref.__init__()=obitools.obo.parser.Xref-class.html#__init__,Method obitools.obo.parser.XrefValue.__init__()=obitools.obo.parser.XrefValue-class.html#__init__,Method obitools.parallel.Task.__init__()=obitools.parallel.Task-class.html#__init__,Method obitools.parallel.TaskPool.__init__()=obitools.parallel.TaskPool-class.html#__init__,Method obitools.parallel.jobqueue.Job.__init__()=obitools.parallel.jobqueue.Job-class.html#__init__,Method obitools.parallel.jobqueue.JobIterator.__init__()=obitools.parallel.jobqueue.JobIterator-class.html#__init__,Method obitools.parallel.jobqueue.JobPool.__init__()=obitools.parallel.jobqueue.JobPool-class.html#__init__,Method obitools.phylogeny.PhylogenicTree.__init__()=obitools.phylogeny.PhylogenicTree-class.html#__init__,Method obitools.seqdb.AnnotatedAASequence.__init__()=obitools.seqdb.AnnotatedAASequence-class.html#__init__,Method obitools.seqdb.AnnotatedNucSequence.__init__()=obitools.seqdb.AnnotatedNucSequence-class.html#__init__,Method obitools.seqdb.AnnotatedSequence.__init__()=obitools.seqdb.AnnotatedSequence-class.html#__init__,Method obitools.seqdb.genbank.GpepSequence.__init__()=obitools.seqdb.genbank.GpepSequence-class.html#__init__,Method obitools.seqdb.genbank.graph.DiGraph.__init__()=obitools.seqdb.genbank.graph.DiGraph-class.html#__init__,Method obitools.seqdb.genbank.graph.Edge.__init__()=obitools.seqdb.genbank.graph.Edge-class.html#__init__,Method obitools.seqdb.genbank.graph.Graph.__init__()=obitools.seqdb.genbank.graph.Graph-class.html#__init__,Method obitools.seqdb.genbank.graph.Indexer.__init__()=obitools.seqdb.genbank.graph.Indexer-class.html#__init__,Method obitools.seqdb.genbank.graph.Node.__init__()=obitools.seqdb.genbank.graph.Node-class.html#__init__,Method obitools.seqdb.genbank.graph.UndirectedGraph.__init__()=obitools.seqdb.genbank.graph.UndirectedGraph-class.html#__init__,Method obitools.seqdb.genbank.graph.dag.DAG.__init__()=obitools.seqdb.genbank.graph.dag.DAG-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIAccession.__init__()=obitools.seqdb.genbank.ncbi.NCBIAccession-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__()=obitools.seqdb.genbank.ncbi.NCBIGenbank-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__()=obitools.seqdb.genbank.ncbi.NCBIGenpep-class.html#__init__,Method obitools.solexa.SolexaFile.__init__()=obitools.solexa.SolexaFile-class.html#__init__,Method obitools.solexa.SolexaSequence.__init__()=obitools.solexa.SolexaSequence-class.html#__init__,Method obitools.svg.Circle.__init__()=obitools.svg.Circle-class.html#__init__,Method obitools.svg.Line.__init__()=obitools.svg.Line-class.html#__init__,Method obitools.svg.Rectangle.__init__()=obitools.svg.Rectangle-class.html#__init__,Method obitools.svg.Scene.__init__()=obitools.svg.Scene-class.html#__init__,Method obitools.svg.Text.__init__()=obitools.svg.Text-class.html#__init__,Method obitools.table.ProjectionIterator.__init__()=obitools.table.ProjectionIterator-class.html#__init__,Method obitools.table.SelectionIterator.__init__()=obitools.table.SelectionIterator-class.html#__init__,Method obitools.table.Table.__init__()=obitools.table.Table-class.html#__init__,Method obitools.table.TableIterator.__init__()=obitools.table.TableIterator-class.html#__init__,Method obitools.table.TableIteratorAsDict.__init__()=obitools.table.TableIteratorAsDict-class.html#__init__,Method obitools.table.TableRow.__init__()=obitools.table.TableRow-class.html#__init__,Method obitools.table.UnionIterator.__init__()=obitools.table.UnionIterator-class.html#__init__,Method obitools.table._Row.__init__()=obitools.table._Row-class.html#__init__,Method obitools.tree.TreeNode.__init__()=obitools.tree.TreeNode-class.html#__init__,Method obitools.utils.CachedDB.__init__()=obitools.utils.CachedDB-class.html#__init__,Method obitools.utils.ColumnFile.__init__()=obitools.utils.ColumnFile-class.html#__init__,Method obitools.zipfile.ZipExtFile.__init__()=obitools.zipfile.ZipExtFile-class.html#__init__,Method obitools.zipfile.ZipFile.__init__()=obitools.zipfile.ZipFile-class.html#__init__,Method obitools.zipfile.ZipInfo.__init__()=obitools.zipfile.ZipInfo-class.html#__init__,Method obitools.zipfile._ZipDecrypter.__init__()=obitools.zipfile._ZipDecrypter-class.html#__init__"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
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|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
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|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
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|
obitools.graph.Node.__init__
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|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
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|
obitools.location.CompositeLocation.__init__
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|
obitools.location.PointLocation.__init__
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|
obitools.location.SimpleLocation.__init__
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obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
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|
obitools.obo.parser.NameValue.__init__
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|
obitools.obo.parser.NamespaceValue.__init__
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|
obitools.obo.parser.OBOEntry.__init__
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obitools.obo.parser.OBOTerm.__init__
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obitools.obo.parser.RelationshipValue.__init__
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obitools.obo.parser.RemarkValue.__init__
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|
obitools.obo.parser.SynonymValue.__init__
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|
obitools.obo.parser.TaggedValue.__init__
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|
obitools.obo.parser.TrailingModifier.__init__
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|
obitools.obo.parser.Xref.__init__
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|
obitools.obo.parser.XrefValue.__init__
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|
obitools.parallel.Task.__init__
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|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
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|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
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|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-17', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</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-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">trailing_modifiers</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>
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|
</div></div><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
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<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
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<a name="trailingModifierFactory"></a><div id="trailingModifierFactory-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="trailingModifierFactory-toggle" onclick="return toggle('trailingModifierFactory');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#trailingModifierFactory">trailingModifierFactory</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="trailingModifierFactory-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="trailingModifierFactory-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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|
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> Dispatcher of trailing modifiers.</tt> </tt>
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<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> @param string: a string from a TaggedValue object with a trailing modifiers signal.</tt> </tt>
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<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> @type string: string</tt> </tt>
|
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<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> @return: a class object</tt> </tt>
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<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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|
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> @note: The dispatcher is currently very simple. Only one case is treated by the function.</tt> </tt>
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<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> `the function returns a class object inherited from the class dict if the trailing modifiers</tt> </tt>
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<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> exist, None if they don't.</tt> </tt>
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|
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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|
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
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<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">trailing_modifiers</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="obitools.obo.parser.TrailingModifier" class="py-name" href="#" onclick="return doclink('link-18', 'TrailingModifier', 'link-15');">TrailingModifier</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">)</tt> </tt>
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<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">trailing_modifiers</tt><tt class="py-op">:</tt> </tt>
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<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
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<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">trailing_modifiers</tt> </tt>
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</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
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<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
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<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## TaggedValue treatment area ##</tt> </tt>
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|
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
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<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
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<a name="TaggedValue"></a><div id="TaggedValue-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="TaggedValue-toggle" onclick="return toggle('TaggedValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.TaggedValue-class.html">TaggedValue</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TaggedValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TaggedValue-expanded"><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-docstring"> A couple 'tag:value' of an OBOEntry.</tt> </tt>
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|
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
|
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<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-19" class="py-name" targets="Variable obitools.obo.parser.TaggedValue._match_value=obitools.obo.parser.TaggedValue-class.html#_match_value"><a title="obitools.obo.parser.TaggedValue._match_value" class="py-name" href="#" onclick="return doclink('link-19', '_match_value', 'link-19');">_match_value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'(("(\\\\"|[^\"])*")|(\\\\"|[^\"]))*?( !| {|$)'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt id="link-20" class="py-name" targets="Variable obitools.obo.parser.TaggedValue._split_comment=obitools.obo.parser.TaggedValue-class.html#_split_comment"><a title="obitools.obo.parser.TaggedValue._split_comment" class="py-name" href="#" onclick="return doclink('link-20', '_split_comment', 'link-20');">_split_comment</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'^!| !'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Variable obitools.obo.parser.TaggedValue._match_quotedString=obitools.obo.parser.TaggedValue-class.html#_match_quotedString"><a title="obitools.obo.parser.TaggedValue._match_quotedString" class="py-name" href="#" onclick="return doclink('link-21', '_match_quotedString', 'link-21');">_match_quotedString</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'(?<=")(\\\\"|[^\"])*(?=")'</tt><tt class="py-op">)</tt> </tt>
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<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt id="link-22" class="py-name" targets="Variable obitools.obo.parser.TaggedValue._match_bracket=obitools.obo.parser.TaggedValue-class.html#_match_bracket"><a title="obitools.obo.parser.TaggedValue._match_bracket" class="py-name" href="#" onclick="return doclink('link-22', '_match_bracket', 'link-22');">_match_bracket</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'\[[^\]]*\]'</tt><tt class="py-op">)</tt> </tt>
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<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
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<a name="TaggedValue.__init__"></a><div id="TaggedValue.__init__-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="TaggedValue.__init__-toggle" onclick="return toggle('TaggedValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.TaggedValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TaggedValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggedValue.__init__-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> Constructor of the class TaggedValue.</tt> </tt>
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<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> @param line: a line of an OBOEntry composed of a tag and a value.</tt> </tt>
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<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> @type line: string</tt> </tt>
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<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> @note: The constructor separates tags from right terms. 'value' is extracted </tt> </tt>
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<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> from right terms using a regular expression (value is at the beginning of the</tt> </tt>
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<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> string, between quotes or not). Then, 'comment' is extracted from the rest of the </tt> </tt>
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<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> string using another regular expression ('comment' is at the end of the string </tt> </tt>
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<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> after a '!'. By default, 'comment' is set to None). Finally, 'trailing_modifiers'</tt> </tt>
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<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> are extracted from the last string using another regular expression.</tt> </tt>
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<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> The tag, the value, the comment and the trailing_modifiers are saved.</tt> </tt>
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<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
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<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">debug</tt><tt class="py-op">(</tt><tt class="py-string">"tagValueParser : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
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<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
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<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment">## by default :</tt> </tt>
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<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">trailing_modifiers</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
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<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt id="link-23" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.comment=obitools.obo.parser.OBOTerm-class.html#comment,Variable obitools.zipfile.ZipInfo.comment=obitools.zipfile.ZipInfo-class.html#comment"><a title="obitools.obo.parser.OBOTerm.comment
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obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-23', 'comment', 'link-23');">comment</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
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<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
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<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment">## the tag is saved. 'right' is composed of the value, the comment and the trailing modifiers</tt> </tt>
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<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tag</tt><tt class="py-op">,</tt><tt class="py-name">rigth</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-number">1</tt><tt class="py-op">)</tt> </tt>
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<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
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<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-comment">## the value is saved</tt> </tt>
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<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name" targets="Class obitools.obo.parser.TaggedValue=obitools.obo.parser.TaggedValue-class.html"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-24', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_value" class="py-name" href="#" onclick="return doclink('link-25', '_match_value', 'link-19');">_match_value</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">rigth</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
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<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">debug</tt><tt class="py-op">(</tt><tt class="py-string">"Extracted value : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">value</tt><tt class="py-op">)</tt> </tt>
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<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
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<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-comment">## if there is a value AND a sign of a comment or trailing modifiers</tt> </tt>
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<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">value</tt> <tt class="py-keyword">and</tt> <tt class="py-name">value</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-keyword">in</tt> <tt class="py-string">'!{'</tt><tt class="py-op">:</tt> </tt>
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<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">lvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">value</tt><tt class="py-op">)</tt> </tt>
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<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-comment">## whatever it is a comment or trailing modifiers, it is saved into 'extra'</tt> </tt>
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<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-26" class="py-name" targets="Variable obitools.zipfile.ZipInfo.extra=obitools.zipfile.ZipInfo-class.html#extra"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-26', 'extra', 'link-26');">extra</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rigth</tt><tt class="py-op">[</tt><tt class="py-name">lvalue</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-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment">## a comment is extracted</tt> </tt>
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<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-27" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-27', 'extra', 'link-26');">extra</a></tt> <tt class="py-op">=</tt><tt id="link-28" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-28', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="obitools.obo.parser.TaggedValue._split_comment" class="py-name" href="#" onclick="return doclink('link-29', '_split_comment', 'link-20');">_split_comment</a></tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-30', 'extra', 'link-26');">extra</a></tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
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<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment">## and saved if it exists</tt> </tt>
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<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-31', 'extra', 'link-26');">extra</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
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<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="obitools.obo.parser.OBOTerm.comment
|
|
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-32', 'comment', 'link-23');">comment</a></tt><tt class="py-op">=</tt><tt id="link-33" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-33', 'extra', 'link-26');">extra</a></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">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
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<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment">## trailing modifiers are extracted</tt> </tt>
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<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-34" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-34', 'extra', 'link-26');">extra</a></tt><tt class="py-op">=</tt><tt id="link-35" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-35', 'extra', 'link-26');">extra</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
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<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">trailing_modifiers</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name" targets="Function obitools.obo.parser.trailingModifierFactory()=obitools.obo.parser-module.html#trailingModifierFactory"><a title="obitools.obo.parser.trailingModifierFactory" class="py-name" href="#" onclick="return doclink('link-36', 'trailingModifierFactory', 'link-36');">trailingModifierFactory</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-37', 'extra', 'link-26');">extra</a></tt><tt class="py-op">)</tt> </tt>
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<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment">## the value is cleaned of any comment or trailing modifiers signals</tt> </tt>
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<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">value</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>
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<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
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<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">'use_term'</tt><tt class="py-op">:</tt> </tt>
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<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">tag</tt><tt class="py-op">=</tt><tt class="py-string">'consider'</tt> </tt>
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<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">,</tt><tt class="py-string">"user_term is a deprecated tag, you should instead use consider"</tt> </tt>
|
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<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
|
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<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-comment">## recording zone</tt> </tt>
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<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt> <tt class="py-op">=</tt><tt class="py-name">value</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-name">tag</tt> </tt>
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<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="obitools.obo.parser.OBOTerm.comment
|
|
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-38', 'comment', 'link-23');">comment</a></tt> </tt>
|
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<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt class="py-name">trailing_modifiers</tt> </tt>
|
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</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
|
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<a name="TaggedValue.__str__"></a><div id="TaggedValue.__str__-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="TaggedValue.__str__-toggle" onclick="return toggle('TaggedValue.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.TaggedValue-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TaggedValue.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggedValue.__str__-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">)</tt> </tt>
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</div><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
|
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<a name="TaggedValue.__repr__"></a><div id="TaggedValue.__repr__-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="TaggedValue.__repr__-toggle" onclick="return toggle('TaggedValue.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.TaggedValue-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="TaggedValue.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggedValue.__repr__-expanded"><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'''"""%s"""'''</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
|
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</div></div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
|
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<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
|
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<a name="NameValue"></a><div id="NameValue-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="NameValue-toggle" onclick="return toggle('NameValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.NameValue-class.html">NameValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="NameValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NameValue-expanded"><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
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<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> A couple 'name:value' inherited from the class TaggedValue. Used to manage name tags.</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>
|
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<a name="NameValue.__init__"></a><div id="NameValue.__init__-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="NameValue.__init__-toggle" onclick="return toggle('NameValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.NameValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="NameValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NameValue.__init__-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
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<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-comment">## no use of the TaggedValue constructor. The NameValue is very simple.</tt> </tt>
|
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<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tag</tt><tt class="py-op">,</tt><tt class="py-name">rigth</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
|
|
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment">## recording zone</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">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">rigth</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</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">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'name'</tt> </tt>
|
|
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
|
|
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
|
|
</div></div><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>
|
|
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
|
|
<a name="DefValue"></a><div id="DefValue-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="DefValue-toggle" onclick="return toggle('DefValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.DefValue-class.html">DefValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="DefValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DefValue-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> A couple 'def:value' inherited from the class TaggedValue. Used to manage def tags.</tt> </tt>
|
|
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
|
|
<a name="DefValue.__init__"></a><div id="DefValue.__init__-def"><a name="L188"></a><tt class="py-lineno">188</tt> <a class="py-toggle" href="#" id="DefValue.__init__-toggle" onclick="return toggle('DefValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.DefValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="DefValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DefValue.__init__-expanded"><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> Constructor of the class DefValue.</tt> </tt>
|
|
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> @param line: a line of an OBOEntry composed of a tag named 'def' and a value.</tt> </tt>
|
|
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> @type line: string</tt> </tt>
|
|
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> @note: The constructor calls the TaggedValue constructor. A regular expression </tt> </tt>
|
|
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> is used to extract the 'definition' from TaggedValue.value (definition is a not </tt> </tt>
|
|
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> quoted TaggedValue.value). A regular expression is used to extract 'dbxrefs' </tt> </tt>
|
|
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> from the aggedValue.value without the definition (dbxrefs are between brackets</tt> </tt>
|
|
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> and definition can be so). Definition is saved as the new value of the DefValue.</tt> </tt>
|
|
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"> dbxrefs are saved.</tt> </tt>
|
|
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
|
|
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-comment">## use of the TaggedValue constructor</tt> </tt>
|
|
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-39" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-39', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-40', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
|
|
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-comment">## definition, which is quoted, is extracted from the standard value of a TaggedValue.</tt> </tt>
|
|
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-41" class="py-name" targets="Variable obitools.BioSequence.definition=obitools.BioSequence-class.html#definition,Variable obitools.WrappedBioSequence.definition=obitools.WrappedBioSequence-class.html#definition,Variable obitools.cns.quality.QualitySequence.definition=obitools.cns.quality.QualitySequence-class.html#definition,Variable obitools.obo.parser.OBOTerm.definition=obitools.obo.parser.OBOTerm-class.html#definition"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-41', 'definition', 'link-41');">definition</a></tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-42', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_quotedString" class="py-name" href="#" onclick="return doclink('link-43', '_match_quotedString', 'link-21');">_match_quotedString</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
|
|
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment">## the standard value is cleaned of the definition.</tt> </tt>
|
|
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cleanvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-44', 'definition', 'link-41');">definition</a></tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">cleanvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">cleanvalue</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
|
|
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment">## dbxrefs are searched into the rest of the standard value.</tt> </tt>
|
|
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dbxrefs</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-45', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_bracket" class="py-name" href="#" onclick="return doclink('link-46', '_match_bracket', 'link-22');">_match_bracket</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">cleanvalue</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
|
|
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment">## recording zone</tt> </tt>
|
|
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## the value of a DefValue is not the standard value but the definition.</tt> </tt>
|
|
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">=</tt><tt id="link-47" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-47', 'definition', 'link-41');">definition</a></tt> </tt>
|
|
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">=</tt><tt id="link-48" class="py-name" targets="Function obitools.obo.parser.xrefFactory()=obitools.obo.parser-module.html#xrefFactory"><a title="obitools.obo.parser.xrefFactory" class="py-name" href="#" onclick="return doclink('link-48', 'xrefFactory', 'link-48');">xrefFactory</a></tt><tt class="py-op">(</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
|
|
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
|
|
<a name="SynonymValue"></a><div id="SynonymValue-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="SynonymValue-toggle" onclick="return toggle('SynonymValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.SynonymValue-class.html">SynonymValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SynonymValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SynonymValue-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> A couple 'synonym:value' inherited from the class TaggedValue. Used to manage </tt> </tt>
|
|
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> synonym tags, exact_synonym tags, broad_synonym tags and narrow_synonym tags.</tt> </tt>
|
|
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt>
|
|
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt id="link-49" class="py-name" targets="Variable obitools.obo.parser.SynonymValue._match_scope=obitools.obo.parser.SynonymValue-class.html#_match_scope"><a title="obitools.obo.parser.SynonymValue._match_scope" class="py-name" href="#" onclick="return doclink('link-49', '_match_scope', 'link-49');">_match_scope</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'(?<="")[^\[]*(?=\[|$)'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
|
|
<a name="SynonymValue.__init__"></a><div id="SynonymValue.__init__-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="SynonymValue.__init__-toggle" onclick="return toggle('SynonymValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.SynonymValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SynonymValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SynonymValue.__init__-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> Constructor of the class SynonymValue.</tt> </tt>
|
|
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> @param line: a line of an OBOEntry composed of a tag named 'synonym' or</tt> </tt>
|
|
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> 'exact_synonym' or 'broad_synonym' or 'narrow_synonym' and a value.</tt> </tt>
|
|
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> @type line: string</tt> </tt>
|
|
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> @note: SynonymValue is composed of a tag, a value, a scope, a list of types and </tt> </tt>
|
|
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> dbxrefs.</tt> </tt>
|
|
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> The constructor calls the TaggedValue constructor. A regular expression </tt> </tt>
|
|
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> is used to extract 'definition' from TaggedValue.value (definition is a not </tt> </tt>
|
|
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> quoted TaggedValue.value). Definition is saved as the new value of the class</tt> </tt>
|
|
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> SynonymValue.</tt> </tt>
|
|
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> A regular expression is used to extract 'attributes' from the rest of the</tt> </tt>
|
|
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> string. Attributes may contain an optional synonym scope and an optional list </tt> </tt>
|
|
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> of synonym types. The scope is extracted from attributes or set by default to</tt> </tt>
|
|
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> 'RELATED'. It is saved as the scope of the class. The types are the rest of the </tt> </tt>
|
|
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> attributes and are saved as the list of types of the class.</tt> </tt>
|
|
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> For deprecated tags 'exact_synonym', 'broad_synonym' and 'narrow_synonym', tag</tt> </tt>
|
|
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> is set to 'synonym' and scope is set respectively to 'EXACT', 'BROAD' and 'NARROW'.</tt> </tt>
|
|
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> A regular expression is used to extract 'dbxrefs' from the TaggedValue.value </tt> </tt>
|
|
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> without the definition (dbxrefs are between brackets and definition can be so).</tt> </tt>
|
|
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> dbxrefs are saved.</tt> </tt>
|
|
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
|
|
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-comment">## use of the TaggedValue constructor</tt> </tt>
|
|
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-50" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-50', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-51', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
|
|
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-comment">## definition, which is quoted, is extracted from the standard value of a TaggedValue.</tt> </tt>
|
|
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-52" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-52', 'definition', 'link-41');">definition</a></tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-53', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_quotedString" class="py-name" href="#" onclick="return doclink('link-54', '_match_quotedString', 'link-21');">_match_quotedString</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
|
|
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment">## the standard value is cleaned of the definition.</tt> </tt>
|
|
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cleanvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-55', 'definition', 'link-41');">definition</a></tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">cleanvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">cleanvalue</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
|
|
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-comment">## 1) attributes are searched into the rest of the standard value.</tt> </tt>
|
|
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## 2) then they are stripped.</tt> </tt>
|
|
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## 3) then they are split on every ' '.</tt> </tt>
|
|
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## 4) finally they are ordered into a set.</tt> </tt>
|
|
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">attributes</tt> <tt class="py-op">=</tt> <tt class="py-name">set</tt><tt class="py-op">(</tt><tt id="link-56" class="py-name" targets="Class obitools.obo.parser.SynonymValue=obitools.obo.parser.SynonymValue-class.html"><a title="obitools.obo.parser.SynonymValue" class="py-name" href="#" onclick="return doclink('link-56', 'SynonymValue', 'link-56');">SynonymValue</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="obitools.obo.parser.SynonymValue._match_scope" class="py-name" href="#" onclick="return doclink('link-57', '_match_scope', 'link-49');">_match_scope</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">cleanvalue</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</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">strip</tt><tt class="py-op">(</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-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
|
|
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-comment">## the scopes are the junction between the attributes and a set of specific terms. </tt> </tt>
|
|
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">scopes</tt> <tt class="py-op">=</tt> <tt class="py-name">attributes</tt> <tt class="py-op">&</tt> <tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'RELATED'</tt><tt class="py-op">,</tt><tt class="py-string">'EXACT'</tt><tt class="py-op">,</tt><tt class="py-string">'BROAD'</tt><tt class="py-op">,</tt><tt class="py-string">'NARROW'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
|
|
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-comment">## the types are the rest of the attributes.</tt> </tt>
|
|
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-58" class="py-name" targets="Variable obitools.blast.BlastResultIterator.types=obitools.blast.BlastResultIterator-class.html#types,Variable obitools.table.ProjectionIterator.types=obitools.table.ProjectionIterator-class.html#types,Variable obitools.table.SelectionIterator.types=obitools.table.SelectionIterator-class.html#types,Variable obitools.table.Table.types=obitools.table.Table-class.html#types,Variable obitools.table.TableIterator.types=obitools.table.TableIterator-class.html#types,Variable obitools.table.TableIteratorAsDict.types=obitools.table.TableIteratorAsDict-class.html#types,Variable obitools.table.TableRow.types=obitools.table.TableRow-class.html#types,Variable obitools.table.UnionIterator.types=obitools.table.UnionIterator-class.html#types,Variable obitools.table.iTableIterator.types=obitools.table.iTableIterator-class.html#types"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-58', 'types', 'link-58');">types</a></tt> <tt class="py-op">=</tt> <tt class="py-name">attributes</tt> <tt class="py-op">-</tt> <tt class="py-name">scopes</tt> </tt>
|
|
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
|
|
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-comment">## this is a constraint of the OBO format</tt> </tt>
|
|
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">scopes</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-string">"Only one synonym scope allowed"</tt> </tt>
|
|
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
|
|
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-comment">## the scope of the SynonymValue is into scopes or set by default to RELATED</tt> </tt>
|
|
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">scopes</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-name">scopes</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method obitools.table.TableRow.pop()=obitools.table.TableRow-class.html#pop,Method obitools.table._Row.pop()=obitools.table._Row-class.html#pop"><a title="obitools.table.TableRow.pop
|
|
obitools.table._Row.pop" class="py-name" href="#" onclick="return doclink('link-59', 'pop', 'link-59');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-string">'RELATED'</tt> </tt>
|
|
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
|
|
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-comment">## Specific rules are defined for the following tags : </tt> </tt>
|
|
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">==</tt> <tt class="py-string">'exact_synonym'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">,</tt><tt class="py-string">'exact_synonym is a deprecated tag use instead synonym tag'</tt> </tt>
|
|
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'synonym'</tt> </tt>
|
|
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-string">'EXACT'</tt> </tt>
|
|
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
|
|
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">==</tt> <tt class="py-string">'broad_synonym'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">,</tt><tt class="py-string">'broad_synonym is a deprecated tag use instead synonym tag'</tt> </tt>
|
|
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'synonym'</tt> </tt>
|
|
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-string">'BROAD'</tt> </tt>
|
|
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
|
|
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">==</tt> <tt class="py-string">'narrow_synonym'</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">raise</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">,</tt><tt class="py-string">'narrow_synonym is a deprecated tag use instead synonym tag'</tt> </tt>
|
|
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'synonym'</tt> </tt>
|
|
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-string">'NARROW'</tt> </tt>
|
|
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> </tt>
|
|
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">==</tt> <tt class="py-string">'systematic_synonym'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-comment">#raise DeprecationWarning,'narrow_synonym is a deprecated tag use instead sysnonym tag'</tt> </tt>
|
|
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'synonym'</tt> </tt>
|
|
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-string">'SYSTEMATIC'</tt> </tt>
|
|
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> </tt>
|
|
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-comment">## this is our own constraint. deprecated tags are not saved by this parser. </tt> </tt>
|
|
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-op">==</tt><tt class="py-string">'synonym'</tt><tt class="py-op">,</tt><tt class="py-string">"%s synonym type is not managed"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> </tt>
|
|
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
|
|
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment">## dbxrefs are searched into the rest of the standard value.</tt> </tt>
|
|
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dbxrefs</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-60', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_bracket" class="py-name" href="#" onclick="return doclink('link-61', '_match_bracket', 'link-22');">_match_bracket</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">cleanvalue</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
|
|
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-comment">## recording zone</tt> </tt>
|
|
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## the value of a SynonymValue is not the standard value but the definition.</tt> </tt>
|
|
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-62', 'definition', 'link-41');">definition</a></tt> </tt>
|
|
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbxrefs</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="obitools.obo.parser.xrefFactory" class="py-name" href="#" onclick="return doclink('link-63', 'xrefFactory', 'link-48');">xrefFactory</a></tt><tt class="py-op">(</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scope</tt> <tt class="py-op">=</tt> <tt class="py-name">scope</tt> </tt>
|
|
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-64', 'types', 'link-58');">types</a></tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-65', 'types', 'link-58');">types</a></tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
|
|
<a name="SynonymValue.__eq__"></a><div id="SynonymValue.__eq__-def"><a name="L321"></a><tt class="py-lineno">321</tt> <a class="py-toggle" href="#" id="SynonymValue.__eq__-toggle" onclick="return toggle('SynonymValue.__eq__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.SynonymValue-class.html#__eq__">__eq__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">b</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SynonymValue.__eq__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SynonymValue.__eq__-expanded"><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scope</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">scope</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-66', 'types', 'link-58');">types</a></tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-67', 'types', 'link-58');">types</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
|
|
<a name="SynonymValue.__hash__"></a><div id="SynonymValue.__hash__-def"><a name="L327"></a><tt class="py-lineno">327</tt> <a class="py-toggle" href="#" id="SynonymValue.__hash__-toggle" onclick="return toggle('SynonymValue.__hash__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.SynonymValue-class.html#__hash__">__hash__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SynonymValue.__hash__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SynonymValue.__hash__-expanded"><a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">hash</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">frozenset</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbxrefs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scope</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">frozenset</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="obitools.blast.BlastResultIterator.types
|
|
obitools.table.ProjectionIterator.types
|
|
obitools.table.SelectionIterator.types
|
|
obitools.table.Table.types
|
|
obitools.table.TableIterator.types
|
|
obitools.table.TableIteratorAsDict.types
|
|
obitools.table.TableRow.types
|
|
obitools.table.UnionIterator.types
|
|
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-68', 'types', 'link-58');">types</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">]</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-op">%</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">**</tt><tt class="py-number">31</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
|
|
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
|
|
<a name="XrefValue"></a><div id="XrefValue-def"><a name="L337"></a><tt class="py-lineno">337</tt> <a class="py-toggle" href="#" id="XrefValue-toggle" onclick="return toggle('XrefValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.XrefValue-class.html">XrefValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="XrefValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="XrefValue-expanded"><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"> A couple 'xref:value' inherited from the class TaggedValue. Used to manage </tt> </tt>
|
|
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"> xref tags.</tt> </tt>
|
|
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
|
|
<a name="XrefValue.__init__"></a><div id="XrefValue.__init__-def"><a name="L343"></a><tt class="py-lineno">343</tt> <a class="py-toggle" href="#" id="XrefValue.__init__-toggle" onclick="return toggle('XrefValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.XrefValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="XrefValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="XrefValue.__init__-expanded"><a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
|
|
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-comment">## use of the TaggedValue constructor</tt> </tt>
|
|
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-69" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-69', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-70', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
|
|
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment">## use the same function as the dbxrefs</tt> </tt>
|
|
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">=</tt><tt id="link-71" class="py-name"><a title="obitools.obo.parser.xrefFactory" class="py-name" href="#" onclick="return doclink('link-71', 'xrefFactory', 'link-48');">xrefFactory</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> </tt>
|
|
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'xref_analog'</tt><tt class="py-op">,</tt><tt class="py-string">'xref_unk'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">,</tt><tt class="py-string">'%s is a deprecated tag use instead sysnonym tag'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> </tt>
|
|
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">=</tt><tt class="py-string">'xref'</tt> </tt>
|
|
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> </tt>
|
|
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-comment">## this is our own constraint. deprecated tags are not saved by this parser. </tt> </tt>
|
|
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">'xref'</tt> </tt>
|
|
</div></div><a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> </tt>
|
|
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt>
|
|
<a name="RelationshipValue"></a><div id="RelationshipValue-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="RelationshipValue-toggle" onclick="return toggle('RelationshipValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.RelationshipValue-class.html">RelationshipValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="RelationshipValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RelationshipValue-expanded"><a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> A couple 'xref:value' inherited from the class TaggedValue. Used to manage </tt> </tt>
|
|
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> xref tags.</tt> </tt>
|
|
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
|
|
<a name="RelationshipValue.__init__"></a><div id="RelationshipValue.__init__-def"><a name="L365"></a><tt class="py-lineno">365</tt> <a class="py-toggle" href="#" id="RelationshipValue.__init__-toggle" onclick="return toggle('RelationshipValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.RelationshipValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="RelationshipValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RelationshipValue.__init__-expanded"><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> </tt>
|
|
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-comment">## use of the TaggedValue constructor</tt> </tt>
|
|
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-72" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-72', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-73', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
|
|
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-comment">## the value is split on the first ' '.</tt> </tt>
|
|
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> </tt>
|
|
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-comment">## succesful split !</tt> </tt>
|
|
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">value</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">relationship</tt><tt class="py-op">=</tt><tt class="py-name">value</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">term</tt><tt class="py-op">=</tt><tt class="py-name">value</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-comment">## unsuccesful split. The relationship is set by default to IS_A</tt> </tt>
|
|
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">relationship</tt><tt class="py-op">=</tt><tt class="py-string">'is_a'</tt> </tt>
|
|
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">term</tt><tt class="py-op">=</tt><tt class="py-name">value</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
|
|
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-comment">## recording zone </tt> </tt>
|
|
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">=</tt><tt class="py-name">term</tt> </tt>
|
|
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">relationship</tt><tt class="py-op">=</tt><tt class="py-name">relationship</tt> </tt>
|
|
</div></div><a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
|
|
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
|
|
<a name="NamespaceValue"></a><div id="NamespaceValue-def"><a name="L387"></a><tt class="py-lineno">387</tt> <a class="py-toggle" href="#" id="NamespaceValue-toggle" onclick="return toggle('NamespaceValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.NamespaceValue-class.html">NamespaceValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="NamespaceValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NamespaceValue-expanded"><a name="NamespaceValue.__init__"></a><div id="NamespaceValue.__init__-def"><a name="L388"></a><tt class="py-lineno">388</tt> <a class="py-toggle" href="#" id="NamespaceValue.__init__-toggle" onclick="return toggle('NamespaceValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.NamespaceValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="NamespaceValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NamespaceValue.__init__-expanded"><a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt id="link-74" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-74', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-75', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
|
|
<a name="RemarkValue"></a><div id="RemarkValue-def"><a name="L391"></a><tt class="py-lineno">391</tt> <a class="py-toggle" href="#" id="RemarkValue-toggle" onclick="return toggle('RemarkValue');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.RemarkValue-class.html">RemarkValue</a><tt class="py-op">(</tt><tt class="py-base-class">TaggedValue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="RemarkValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RemarkValue-expanded"><a name="RemarkValue.__init__"></a><div id="RemarkValue.__init__-def"><a name="L392"></a><tt class="py-lineno">392</tt> <a class="py-toggle" href="#" id="RemarkValue.__init__-toggle" onclick="return toggle('RemarkValue.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.RemarkValue-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="RemarkValue.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RemarkValue.__init__-expanded"><a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-76', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-77', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt id="link-78" class="py-name" targets="Variable obitools.graph.Node.label=obitools.graph.Node-class.html#label,Variable obitools.phylogeny.PhylogenicNode.label=obitools.phylogeny.PhylogenicNode-class.html#label,Variable obitools.seqdb.genbank.graph.Node.label=obitools.seqdb.genbank.graph.Node-class.html#label"><a title="obitools.graph.Node.label
|
|
obitools.phylogeny.PhylogenicNode.label
|
|
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-78', 'label', 'link-78');">label</a></tt><tt class="py-op">,</tt><tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</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-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="obitools.graph.Node.label
|
|
obitools.phylogeny.PhylogenicNode.label
|
|
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-79', 'label', 'link-78');">label</a></tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="obitools.graph.Node.label
|
|
obitools.phylogeny.PhylogenicNode.label
|
|
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-80', 'label', 'link-78');">label</a></tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">value</tt><tt class="py-op">=</tt><tt class="py-name">value</tt> </tt>
|
|
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="obitools.graph.Node.label
|
|
obitools.phylogeny.PhylogenicNode.label
|
|
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-81', 'label', 'link-78');">label</a></tt><tt class="py-op">=</tt><tt id="link-82" class="py-name"><a title="obitools.graph.Node.label
|
|
obitools.phylogeny.PhylogenicNode.label
|
|
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-82', 'label', 'link-78');">label</a></tt> </tt>
|
|
</div></div><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
|
|
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> </tt>
|
|
<a name="taggedValueFactory"></a><div id="taggedValueFactory-def"><a name="L401"></a><tt class="py-lineno">401</tt> <a class="py-toggle" href="#" id="taggedValueFactory-toggle" onclick="return toggle('taggedValueFactory');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#taggedValueFactory">taggedValueFactory</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="taggedValueFactory-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="taggedValueFactory-expanded"><a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-docstring"> A function used to dispatch lines of an OBOEntry between the class TaggedValue</tt> </tt>
|
|
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"> and its inherited classes.</tt> </tt>
|
|
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> @param line: a line of an OBOEntry composed of a tag and a value.</tt> </tt>
|
|
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> @type line: string</tt> </tt>
|
|
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"> @return: a class object</tt> </tt>
|
|
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> </tt>
|
|
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'namespace'</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">17</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'default-namespace'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-83" class="py-name" targets="Class obitools.obo.parser.NamespaceValue=obitools.obo.parser.NamespaceValue-class.html"><a title="obitools.obo.parser.NamespaceValue" class="py-name" href="#" onclick="return doclink('link-83', 'NamespaceValue', 'link-83');">NamespaceValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-comment">## DefValue is an inherited class of TaggedValue</tt> </tt>
|
|
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'def'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-84" class="py-name" targets="Class obitools.obo.parser.DefValue=obitools.obo.parser.DefValue-class.html"><a title="obitools.obo.parser.DefValue" class="py-name" href="#" onclick="return doclink('link-84', 'DefValue', 'link-84');">DefValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-comment">## SynonymValue is an inherited class of TaggedValue</tt> </tt>
|
|
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"synonym"</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">14</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-string">"synonymtypedef"</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">13</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"exact_synonym"</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">13</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"broad_synonym"</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">14</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"narrow_synonym"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-85" class="py-name"><a title="obitools.obo.parser.SynonymValue" class="py-name" href="#" onclick="return doclink('link-85', 'SynonymValue', 'link-56');">SynonymValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-comment">## XrefValue is an inherited class of TaggedValue</tt> </tt>
|
|
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'xref'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-86" class="py-name" targets="Class obitools.obo.parser.XrefValue=obitools.obo.parser.XrefValue-class.html"><a title="obitools.obo.parser.XrefValue" class="py-name" href="#" onclick="return doclink('link-86', 'XrefValue', 'link-86');">XrefValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-comment">## NameValue is an inherited class of TaggedValue</tt> </tt>
|
|
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'name'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-87" class="py-name" targets="Class obitools.obo.parser.NameValue=obitools.obo.parser.NameValue-class.html"><a title="obitools.obo.parser.NameValue" class="py-name" href="#" onclick="return doclink('link-87', 'NameValue', 'link-87');">NameValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-comment">## RelationshipValue is an inherited class of TaggedValue</tt> </tt>
|
|
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">15</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'intersection_of'</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt><tt class="py-string">'union_of'</tt> <tt class="py-keyword">or</tt> </tt>
|
|
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">12</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'relationship'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-88" class="py-name" targets="Class obitools.obo.parser.RelationshipValue=obitools.obo.parser.RelationshipValue-class.html"><a title="obitools.obo.parser.RelationshipValue" class="py-name" href="#" onclick="return doclink('link-88', 'RelationshipValue', 'link-88');">RelationshipValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'remark'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-89" class="py-name" targets="Class obitools.obo.parser.RemarkValue=obitools.obo.parser.RemarkValue-class.html"><a title="obitools.obo.parser.RemarkValue" class="py-name" href="#" onclick="return doclink('link-89', 'RemarkValue', 'link-89');">RemarkValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
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<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-comment">## each line is a couple : tag / value (and some more features)</tt> </tt>
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<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
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<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-90" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-90', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
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</div><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> </tt>
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|
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
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<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## Xref treatment area ##</tt> </tt>
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<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#################################################################################</tt> </tt>
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<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
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<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> </tt>
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<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> </tt>
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<a name="Xref"></a><div id="Xref-def"><a name="L448"></a><tt class="py-lineno">448</tt> <a class="py-toggle" href="#" id="Xref-toggle" onclick="return toggle('Xref');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.Xref-class.html">Xref</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="Xref-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Xref-expanded"><a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> A xref object of an OBOentry. It may be the 'dbxrefs' of SynonymValue and </tt> </tt>
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<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> DefValue objects or the 'value' of XrefValue objects.</tt> </tt>
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<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
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<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt id="link-91" class="py-name" targets="Variable obitools.obo.parser.Xref.__splitdata__=obitools.obo.parser.Xref-class.html#__splitdata__"><a title="obitools.obo.parser.Xref.__splitdata__" class="py-name" href="#" onclick="return doclink('link-91', '__splitdata__', 'link-91');">__splitdata__</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">' +(?=["{])'</tt><tt class="py-op">)</tt> </tt>
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<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> </tt>
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<a name="Xref.__init__"></a><div id="Xref.__init__-def"><a name="L456"></a><tt class="py-lineno">456</tt> <a class="py-toggle" href="#" id="Xref.__init__-toggle" onclick="return toggle('Xref.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.Xref-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">ref</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="Xref.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Xref.__init__-expanded"><a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ref</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">:</tt> <tt class="py-comment">#</tt> </tt>
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<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> <tt class="py-comment">#</tt> </tt>
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<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment">#</tt> </tt>
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<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> <tt class="py-comment"># Modifs JJ sinon erreur : list index out of range</tt> </tt>
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<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name" targets="Class obitools.obo.parser.Xref=obitools.obo.parser.Xref-class.html"><a title="obitools.obo.parser.Xref" class="py-name" href="#" onclick="return doclink('link-92', 'Xref', 'link-92');">Xref</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="obitools.obo.parser.Xref.__splitdata__" class="py-name" href="#" onclick="return doclink('link-93', '__splitdata__', 'link-91');">__splitdata__</a></tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">ref</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-comment">#</tt> </tt>
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<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">ref</tt> <tt class="py-op">=</tt> <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-comment">#</tt> </tt>
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<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-name">description</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
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<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">trailing_modifiers</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
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|
<a name="L465"></a><tt class="py-lineno">465</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">data</tt><tt class="py-op">)</tt><tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
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|
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt id="link-94" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-94', 'extra', 'link-26');">extra</a></tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
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|
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">description</tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name"><a title="obitools.obo.parser.TaggedValue" class="py-name" href="#" onclick="return doclink('link-95', 'TaggedValue', 'link-24');">TaggedValue</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="obitools.obo.parser.TaggedValue._match_quotedString" class="py-name" href="#" onclick="return doclink('link-96', '_match_quotedString', 'link-21');">_match_quotedString</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-97', 'extra', 'link-26');">extra</a></tt><tt class="py-op">)</tt> </tt>
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<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">description</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
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<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">description</tt> <tt class="py-op">=</tt> <tt class="py-name">description</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
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<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt id="link-98" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-98', 'extra', 'link-26');">extra</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-name">description</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
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<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt id="link-99" class="py-name"><a title="obitools.obo.parser.trailingModifierFactory" class="py-name" href="#" onclick="return doclink('link-99', 'trailingModifierFactory', 'link-36');">trailingModifierFactory</a></tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="obitools.zipfile.ZipInfo.extra" class="py-name" href="#" onclick="return doclink('link-100', 'extra', 'link-26');">extra</a></tt><tt class="py-op">)</tt> </tt>
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|
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference</tt><tt class="py-op">=</tt><tt class="py-name">ref</tt> </tt>
|
|
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">description</tt><tt class="py-op">=</tt><tt class="py-name">description</tt> </tt>
|
|
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">=</tt><tt class="py-name">trailing_modifiers</tt> </tt>
|
|
</div><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> </tt>
|
|
<a name="Xref.__eq__"></a><div id="Xref.__eq__-def"><a name="L476"></a><tt class="py-lineno">476</tt> <a class="py-toggle" href="#" id="Xref.__eq__-toggle" onclick="return toggle('Xref.__eq__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.Xref-class.html#__eq__">__eq__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">b</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Xref.__eq__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Xref.__eq__-expanded"><a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">reference</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">description</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">description</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> </tt>
|
|
<a name="Xref.__hash__"></a><div id="Xref.__hash__-def"><a name="L480"></a><tt class="py-lineno">480</tt> <a class="py-toggle" href="#" id="Xref.__hash__-toggle" onclick="return toggle('Xref.__hash__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.Xref-class.html#__hash__">__hash__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Xref.__hash__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Xref.__hash__-expanded"><a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">hash</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">description</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailing_modifiers</tt><tt class="py-op">]</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-op">%</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">**</tt><tt class="py-number">31</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> </tt>
|
|
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> </tt>
|
|
<a name="xrefFactory"></a><div id="xrefFactory-def"><a name="L486"></a><tt class="py-lineno">486</tt> <a class="py-toggle" href="#" id="xrefFactory-toggle" onclick="return toggle('xrefFactory');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#xrefFactory">xrefFactory</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="xrefFactory-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="xrefFactory-expanded"><a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-docstring"> Dispatcher of xrefs.</tt> </tt>
|
|
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-docstring"> @param string: a string (between brackets) from an inherited TaggedValue object with a dbxrefs </tt> </tt>
|
|
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"> signal (actually, the signal can only be found into SynonymValue and DefValue </tt> </tt>
|
|
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"> objects) or a string (without brackets) from a XrefValue object.</tt> </tt>
|
|
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> @type string: string</tt> </tt>
|
|
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-docstring"> @return: a class object</tt> </tt>
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|
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-docstring"> @note: The dispatcher treats differently the strings between brackets (from SynonymValue and </tt> </tt>
|
|
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-docstring"> DefValue objects) and without brackets (from XrefValue objects).</tt> </tt>
|
|
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> </tt>
|
|
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">string</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'['</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-101" class="py-name"><a title="obitools.obo.parser.Xref" class="py-name" href="#" onclick="return doclink('link-101', 'Xref', 'link-92');">Xref</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">string</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-number">1</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>
|
|
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-102" class="py-name"><a title="obitools.obo.parser.Xref" class="py-name" href="#" onclick="return doclink('link-102', 'Xref', 'link-92');">Xref</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> </tt>
|
|
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> </tt>
|
|
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"><tt class="py-comment">#################################################################################</tt> </tt>
|
|
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## Stanza treatment area ##</tt> </tt>
|
|
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#################################################################################</tt> </tt>
|
|
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
|
|
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOEntry"></a><div id="OBOEntry-def"><a name="L513"></a><tt class="py-lineno">513</tt> <a class="py-toggle" href="#" id="OBOEntry-toggle" onclick="return toggle('OBOEntry');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.OBOEntry-class.html">OBOEntry</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOEntry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OBOEntry-expanded"><a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-docstring"> An entry of an OBOFile. It can be a header (without a stanza name) or</tt> </tt>
|
|
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-docstring"> a stanza (with a stanza name between brackets). It inherits from the class dict.</tt> </tt>
|
|
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt id="link-103" class="py-name" targets="Variable obitools.obo.parser.OBOEntry._match_stanza_name=obitools.obo.parser.OBOEntry-class.html#_match_stanza_name"><a title="obitools.obo.parser.OBOEntry._match_stanza_name" class="py-name" href="#" onclick="return doclink('link-103', '_match_stanza_name', 'link-103');">_match_stanza_name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'(?<=^\[)[^\]]*(?=\])'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOEntry.__init__"></a><div id="OBOEntry.__init__-def"><a name="L520"></a><tt class="py-lineno">520</tt> <a class="py-toggle" href="#" id="OBOEntry.__init__-toggle" onclick="return toggle('OBOEntry.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOEntry-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">stanza</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOEntry.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOEntry.__init__-expanded"><a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-comment">## tests if it is the header of the OBO file (returns TRUE) or not (returns FALSE)</tt> </tt>
|
|
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">isHeader</tt> <tt class="py-op">=</tt> <tt class="py-name">stanza</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-string">'['</tt> </tt>
|
|
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">stanza</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-comment">## not the header : there is a [stanzaName]</tt> </tt>
|
|
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">isHeader</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stanzaName</tt> <tt class="py-op">=</tt> <tt class="py-name">lines</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">strip</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-number">1</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">=</tt><tt class="py-name">lines</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="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-comment">## whatever the stanza is. </tt> </tt>
|
|
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-comment">## each line is a couple : tag / value</tt> </tt>
|
|
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">taggedvalue</tt> <tt class="py-op">=</tt> <tt id="link-104" class="py-name" targets="Function obitools.obo.parser.taggedValueFactory()=obitools.obo.parser-module.html#taggedValueFactory"><a title="obitools.obo.parser.taggedValueFactory" class="py-name" href="#" onclick="return doclink('link-104', 'taggedValueFactory', 'link-104');">taggedValueFactory</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">taggedvalue</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">taggedvalue</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
|
|
obitools.table.Table.append
|
|
obitools.table.TableRow.append
|
|
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-105', 'append', 'link-105');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">taggedvalue</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">taggedvalue</tt><tt class="py-op">.</tt><tt class="py-name">tag</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">taggedvalue</tt><tt class="py-op">]</tt> </tt>
|
|
</div><a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOEntry.parseStanzaName"></a><div id="OBOEntry.parseStanzaName-def"><a name="L537"></a><tt class="py-lineno">537</tt> <a class="py-toggle" href="#" id="OBOEntry.parseStanzaName-toggle" onclick="return toggle('OBOEntry.parseStanzaName');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOEntry-class.html#parseStanzaName">parseStanzaName</a><tt class="py-op">(</tt><tt class="py-param">stanza</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOEntry.parseStanzaName-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOEntry.parseStanzaName-expanded"><a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-name">sm</tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name" targets="Class obitools.obo.parser.OBOEntry=obitools.obo.parser.OBOEntry-class.html"><a title="obitools.obo.parser.OBOEntry" class="py-name" href="#" onclick="return doclink('link-106', 'OBOEntry', 'link-106');">OBOEntry</a></tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="obitools.obo.parser.OBOEntry._match_stanza_name" class="py-name" href="#" onclick="return doclink('link-107', '_match_stanza_name', 'link-103');">_match_stanza_name</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">stanza</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sm</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sm</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
|
|
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt id="link-108" class="py-name" targets="Static Method obitools.obo.parser.OBOEntry.parseStanzaName()=obitools.obo.parser.OBOEntry-class.html#parseStanzaName"><a title="obitools.obo.parser.OBOEntry.parseStanzaName" class="py-name" href="#" onclick="return doclink('link-108', 'parseStanzaName', 'link-108');">parseStanzaName</a></tt><tt class="py-op">=</tt><tt class="py-name">staticmethod</tt><tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="obitools.obo.parser.OBOEntry.parseStanzaName" class="py-name" href="#" onclick="return doclink('link-109', 'parseStanzaName', 'link-108');">parseStanzaName</a></tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> </tt>
|
|
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> </tt>
|
|
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm"></a><div id="OBOTerm-def"><a name="L548"></a><tt class="py-lineno">548</tt> <a class="py-toggle" href="#" id="OBOTerm-toggle" onclick="return toggle('OBOTerm');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html">OBOTerm</a><tt class="py-op">(</tt><tt class="py-base-class">OBOEntry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OBOTerm-expanded"><a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"><tt class="py-docstring"> A stanza named 'Term'. It inherits from the class OBOEntry.</tt> </tt>
|
|
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="OBOTerm.__init__"></a><div id="OBOTerm.__init__-def"><a name="L552"></a><tt class="py-lineno">552</tt> <a class="py-toggle" href="#" id="OBOTerm.__init__-toggle" onclick="return toggle('OBOTerm.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-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">stanza</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm.__init__-expanded"><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt>
|
|
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-comment">## use of the OBOEntry constructor.</tt> </tt>
|
|
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-110" class="py-name"><a title="obitools.obo.parser.OBOEntry" class="py-name" href="#" onclick="return doclink('link-110', 'OBOEntry', 'link-106');">OBOEntry</a></tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="obitools.BioSequence.__init__
|
|
obitools.WrappedBioSequence.__init__
|
|
obitools.WrapperSetIterator.__init__
|
|
obitools.align.ssearch.SsearchParser.__init__
|
|
obitools.blast.Blast.__init__
|
|
obitools.blast.BlastCovMinFilter.__init__
|
|
obitools.blast.BlastResultIterator.__init__
|
|
obitools.blast.NetBlast.__init__
|
|
obitools.cns.quality.QualitySequence.__init__
|
|
obitools.distances.DistanceMatrix.__init__
|
|
obitools.ecopcr.EcoPCRFile.__init__
|
|
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
|
|
obitools.ecopcr.taxonomy.Taxonomy.__init__
|
|
obitools.eutils.EFetch.__init__
|
|
obitools.eutils.EUtils.__init__
|
|
obitools.fast.Fast.__init__
|
|
obitools.format.genericparser.GenericParser.__init__
|
|
obitools.graph.DiGraph.__init__
|
|
obitools.graph.Edge.__init__
|
|
obitools.graph.Graph.__init__
|
|
obitools.graph.Indexer.__init__
|
|
obitools.graph.Node.__init__
|
|
obitools.graph.UndirectedGraph.__init__
|
|
obitools.graph.dag.DAG.__init__
|
|
obitools.gzip.GzipFile.__init__
|
|
obitools.location.ComplementLocation.__init__
|
|
obitools.location.CompositeLocation.__init__
|
|
obitools.location.PointLocation.__init__
|
|
obitools.location.SimpleLocation.__init__
|
|
obitools.location.feature.Feature.__init__
|
|
obitools.obo.parser.DefValue.__init__
|
|
obitools.obo.parser.NameValue.__init__
|
|
obitools.obo.parser.NamespaceValue.__init__
|
|
obitools.obo.parser.OBOEntry.__init__
|
|
obitools.obo.parser.OBOTerm.__init__
|
|
obitools.obo.parser.RelationshipValue.__init__
|
|
obitools.obo.parser.RemarkValue.__init__
|
|
obitools.obo.parser.SynonymValue.__init__
|
|
obitools.obo.parser.TaggedValue.__init__
|
|
obitools.obo.parser.TrailingModifier.__init__
|
|
obitools.obo.parser.Xref.__init__
|
|
obitools.obo.parser.XrefValue.__init__
|
|
obitools.parallel.Task.__init__
|
|
obitools.parallel.TaskPool.__init__
|
|
obitools.parallel.jobqueue.Job.__init__
|
|
obitools.parallel.jobqueue.JobIterator.__init__
|
|
obitools.parallel.jobqueue.JobPool.__init__
|
|
obitools.phylogeny.PhylogenicTree.__init__
|
|
obitools.seqdb.AnnotatedAASequence.__init__
|
|
obitools.seqdb.AnnotatedNucSequence.__init__
|
|
obitools.seqdb.AnnotatedSequence.__init__
|
|
obitools.seqdb.genbank.GpepSequence.__init__
|
|
obitools.seqdb.genbank.graph.DiGraph.__init__
|
|
obitools.seqdb.genbank.graph.Edge.__init__
|
|
obitools.seqdb.genbank.graph.Graph.__init__
|
|
obitools.seqdb.genbank.graph.Indexer.__init__
|
|
obitools.seqdb.genbank.graph.Node.__init__
|
|
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
|
|
obitools.seqdb.genbank.graph.dag.DAG.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
|
|
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
|
|
obitools.solexa.SolexaFile.__init__
|
|
obitools.solexa.SolexaSequence.__init__
|
|
obitools.svg.Circle.__init__
|
|
obitools.svg.Line.__init__
|
|
obitools.svg.Rectangle.__init__
|
|
obitools.svg.Scene.__init__
|
|
obitools.svg.Text.__init__
|
|
obitools.table.ProjectionIterator.__init__
|
|
obitools.table.SelectionIterator.__init__
|
|
obitools.table.Table.__init__
|
|
obitools.table.TableIterator.__init__
|
|
obitools.table.TableIteratorAsDict.__init__
|
|
obitools.table.TableRow.__init__
|
|
obitools.table.UnionIterator.__init__
|
|
obitools.table._Row.__init__
|
|
obitools.tree.TreeNode.__init__
|
|
obitools.utils.CachedDB.__init__
|
|
obitools.utils.ColumnFile.__init__
|
|
obitools.zipfile.ZipExtFile.__init__
|
|
obitools.zipfile.ZipFile.__init__
|
|
obitools.zipfile.ZipInfo.__init__
|
|
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-111', '__init__', 'link-17');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">stanza</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> </tt>
|
|
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stanzaName</tt><tt class="py-op">==</tt><tt class="py-string">'Term'</tt> </tt>
|
|
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'id'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'id'</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-string">"An OBOTerm must have an id"</tt> </tt>
|
|
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'name'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'name'</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-string">"An OBOTerm must have a name"</tt> </tt>
|
|
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> </tt>
|
|
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'def'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'def'</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-string">"Only one definition is allowed for an OBO term"</tt> </tt>
|
|
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'comment'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'comment'</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-string">"Only one comment is allowed for an OBO term"</tt> </tt>
|
|
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> </tt>
|
|
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'union_of'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'union_of'</tt><tt class="py-op">]</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-string">"Only one union relationship is allowed for an OBO term"</tt> </tt>
|
|
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'intersection_of'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'intersection_of'</tt><tt class="py-op">]</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-string">"Only one intersection relationship is allowed for an OBO term"</tt> </tt>
|
|
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> </tt>
|
|
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method obitools.obo.parser.OBOTerm._isObsolete()=obitools.obo.parser.OBOTerm-class.html#_isObsolete"><a title="obitools.obo.parser.OBOTerm._isObsolete" class="py-name" href="#" onclick="return doclink('link-112', '_isObsolete', 'link-112');">_isObsolete</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'is_a'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
|
|
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'relationship'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
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|
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'inverse_of'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
|
|
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'disjoint_from'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
|
|
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'union_of'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
|
|
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'intersection_of'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> </tt>
|
|
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> </tt>
|
|
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'replace_by'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="obitools.obo.parser.OBOTerm._isObsolete" class="py-name" href="#" onclick="return doclink('link-113', '_isObsolete', 'link-112');">_isObsolete</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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|
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'consider'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="obitools.obo.parser.OBOTerm._isObsolete" class="py-name" href="#" onclick="return doclink('link-114', '_isObsolete', 'link-112');">_isObsolete</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> </tt>
|
|
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-comment">## make-up functions. </tt> </tt>
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|
<a name="OBOTerm._getDefinition"></a><div id="OBOTerm._getDefinition-def"><a name="L579"></a><tt class="py-lineno">579</tt> <a class="py-toggle" href="#" id="OBOTerm._getDefinition-toggle" onclick="return toggle('OBOTerm._getDefinition');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getDefinition">_getDefinition</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="OBOTerm._getDefinition-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getDefinition-expanded"><a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'def'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
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<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'def'</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="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> </tt>
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|
<a name="OBOTerm._getId"></a><div id="OBOTerm._getId-def"><a name="L584"></a><tt class="py-lineno">584</tt> <a class="py-toggle" href="#" id="OBOTerm._getId-toggle" onclick="return toggle('OBOTerm._getId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getId">_getId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="OBOTerm._getId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getId-expanded"><a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'id'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
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|
</div><a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> </tt>
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|
<a name="OBOTerm._getName"></a><div id="OBOTerm._getName-def"><a name="L587"></a><tt class="py-lineno">587</tt> <a class="py-toggle" href="#" id="OBOTerm._getName-toggle" onclick="return toggle('OBOTerm._getName');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getName">_getName</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="OBOTerm._getName-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getName-expanded"><a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
|
|
</div><a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getComment"></a><div id="OBOTerm._getComment-def"><a name="L590"></a><tt class="py-lineno">590</tt> <a class="py-toggle" href="#" id="OBOTerm._getComment-toggle" onclick="return toggle('OBOTerm._getComment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getComment">_getComment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getComment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getComment-expanded"><a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'comment'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'comment'</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="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getAltIds"></a><div id="OBOTerm._getAltIds-def"><a name="L595"></a><tt class="py-lineno">595</tt> <a class="py-toggle" href="#" id="OBOTerm._getAltIds-toggle" onclick="return toggle('OBOTerm._getAltIds');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getAltIds">_getAltIds</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getAltIds-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getAltIds-expanded"><a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'alt_id'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name" targets="Method obitools.eutils.EFetch.get()=obitools.eutils.EFetch-class.html#get"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-115', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'alt_id'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getIsA"></a><div id="OBOTerm._getIsA-def"><a name="L600"></a><tt class="py-lineno">600</tt> <a class="py-toggle" href="#" id="OBOTerm._getIsA-toggle" onclick="return toggle('OBOTerm._getIsA');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getIsA">_getIsA</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getIsA-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getIsA-expanded"><a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-116', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'is_a'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getSynonym"></a><div id="OBOTerm._getSynonym-def"><a name="L603"></a><tt class="py-lineno">603</tt> <a class="py-toggle" href="#" id="OBOTerm._getSynonym-toggle" onclick="return toggle('OBOTerm._getSynonym');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getSynonym">_getSynonym</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
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</div><div id="OBOTerm._getSynonym-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getSynonym-expanded"><a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'synonym'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-op">:</tt> </tt>
|
|
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-117', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'synonym'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getSubset"></a><div id="OBOTerm._getSubset-def"><a name="L608"></a><tt class="py-lineno">608</tt> <a class="py-toggle" href="#" id="OBOTerm._getSubset-toggle" onclick="return toggle('OBOTerm._getSubset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getSubset">_getSubset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getSubset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getSubset-expanded"><a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-118', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'subset'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getXref"></a><div id="OBOTerm._getXref-def"><a name="L611"></a><tt class="py-lineno">611</tt> <a class="py-toggle" href="#" id="OBOTerm._getXref-toggle" onclick="return toggle('OBOTerm._getXref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getXref">_getXref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getXref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getXref-expanded"><a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-119', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'xref'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getUnion"></a><div id="OBOTerm._getUnion-def"><a name="L614"></a><tt class="py-lineno">614</tt> <a class="py-toggle" href="#" id="OBOTerm._getUnion-toggle" onclick="return toggle('OBOTerm._getUnion');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getUnion">_getUnion</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getUnion-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getUnion-expanded"><a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-120', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'union_of'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getIntersection"></a><div id="OBOTerm._getIntersection-def"><a name="L617"></a><tt class="py-lineno">617</tt> <a class="py-toggle" href="#" id="OBOTerm._getIntersection-toggle" onclick="return toggle('OBOTerm._getIntersection');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getIntersection">_getIntersection</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getIntersection-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getIntersection-expanded"><a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-121', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'intersection_of'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getDisjonction"></a><div id="OBOTerm._getDisjonction-def"><a name="L620"></a><tt class="py-lineno">620</tt> <a class="py-toggle" href="#" id="OBOTerm._getDisjonction-toggle" onclick="return toggle('OBOTerm._getDisjonction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getDisjonction">_getDisjonction</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getDisjonction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getDisjonction-expanded"><a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-122', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'disjoint_from'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._isObsolete"></a><div id="OBOTerm._isObsolete-def"><a name="L623"></a><tt class="py-lineno">623</tt> <a class="py-toggle" href="#" id="OBOTerm._isObsolete-toggle" onclick="return toggle('OBOTerm._isObsolete');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_isObsolete">_isObsolete</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._isObsolete-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._isObsolete-expanded"><a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'is_obsolete'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt> <tt class="py-keyword">and</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-string">'is_obsolete'</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-op">==</tt><tt class="py-string">'true'</tt> </tt>
|
|
</div><a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getReplaceBy"></a><div id="OBOTerm._getReplaceBy-def"><a name="L626"></a><tt class="py-lineno">626</tt> <a class="py-toggle" href="#" id="OBOTerm._getReplaceBy-toggle" onclick="return toggle('OBOTerm._getReplaceBy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getReplaceBy">_getReplaceBy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getReplaceBy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getReplaceBy-expanded"><a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-123', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'replace_by'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOTerm._getConsider"></a><div id="OBOTerm._getConsider-def"><a name="L629"></a><tt class="py-lineno">629</tt> <a class="py-toggle" href="#" id="OBOTerm._getConsider-toggle" onclick="return toggle('OBOTerm._getConsider');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser.OBOTerm-class.html#_getConsider">_getConsider</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOTerm._getConsider-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OBOTerm._getConsider-expanded"><a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-124', 'get', 'link-115');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'consider'</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> </tt>
|
|
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-comment">## automatically make-up !</tt> </tt>
|
|
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-125" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-125', 'definition', 'link-41');">definition</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-126" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getDefinition()=obitools.obo.parser.OBOTerm-class.html#_getDefinition"><a title="obitools.obo.parser.OBOTerm._getDefinition" class="py-name" href="#" onclick="return doclink('link-126', '_getDefinition', 'link-126');">_getDefinition</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt id="link-127" class="py-name" targets="Variable obitools.BioSequence.id=obitools.BioSequence-class.html#id,Variable obitools.cns.quality.QualitySequence.id=obitools.cns.quality.QualitySequence-class.html#id,Variable obitools.obo.parser.OBOTerm.id=obitools.obo.parser.OBOTerm-class.html#id"><a title="obitools.BioSequence.id
|
|
obitools.cns.quality.QualitySequence.id
|
|
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-127', 'id', 'link-127');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-128" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getId()=obitools.obo.parser.OBOTerm-class.html#_getId"><a title="obitools.obo.parser.OBOTerm._getId" class="py-name" href="#" onclick="return doclink('link-128', '_getId', 'link-128');">_getId</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt id="link-129" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.name=obitools.obo.parser.OBOTerm-class.html#name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-129', 'name', 'link-129');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-130" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getName()=obitools.obo.parser.OBOTerm-class.html#_getName"><a title="obitools.obo.parser.OBOTerm._getName" class="py-name" href="#" onclick="return doclink('link-130', '_getName', 'link-130');">_getName</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt id="link-131" class="py-name"><a title="obitools.obo.parser.OBOTerm.comment
|
|
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-131', 'comment', 'link-23');">comment</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-132" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getComment()=obitools.obo.parser.OBOTerm-class.html#_getComment"><a title="obitools.obo.parser.OBOTerm._getComment" class="py-name" href="#" onclick="return doclink('link-132', '_getComment', 'link-132');">_getComment</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt id="link-133" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.alt_ids=obitools.obo.parser.OBOTerm-class.html#alt_ids"><a title="obitools.obo.parser.OBOTerm.alt_ids" class="py-name" href="#" onclick="return doclink('link-133', 'alt_ids', 'link-133');">alt_ids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-134" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getAltIds()=obitools.obo.parser.OBOTerm-class.html#_getAltIds"><a title="obitools.obo.parser.OBOTerm._getAltIds" class="py-name" href="#" onclick="return doclink('link-134', '_getAltIds', 'link-134');">_getAltIds</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt id="link-135" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.is_a=obitools.obo.parser.OBOTerm-class.html#is_a"><a title="obitools.obo.parser.OBOTerm.is_a" class="py-name" href="#" onclick="return doclink('link-135', 'is_a', 'link-135');">is_a</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-136" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getIsA()=obitools.obo.parser.OBOTerm-class.html#_getIsA"><a title="obitools.obo.parser.OBOTerm._getIsA" class="py-name" href="#" onclick="return doclink('link-136', '_getIsA', 'link-136');">_getIsA</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt id="link-137" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.synonyms=obitools.obo.parser.OBOTerm-class.html#synonyms"><a title="obitools.obo.parser.OBOTerm.synonyms" class="py-name" href="#" onclick="return doclink('link-137', 'synonyms', 'link-137');">synonyms</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-138" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getSynonym()=obitools.obo.parser.OBOTerm-class.html#_getSynonym"><a title="obitools.obo.parser.OBOTerm._getSynonym" class="py-name" href="#" onclick="return doclink('link-138', '_getSynonym', 'link-138');">_getSynonym</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt id="link-139" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.subsets=obitools.obo.parser.OBOTerm-class.html#subsets"><a title="obitools.obo.parser.OBOTerm.subsets" class="py-name" href="#" onclick="return doclink('link-139', 'subsets', 'link-139');">subsets</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-140" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getSubset()=obitools.obo.parser.OBOTerm-class.html#_getSubset"><a title="obitools.obo.parser.OBOTerm._getSubset" class="py-name" href="#" onclick="return doclink('link-140', '_getSubset', 'link-140');">_getSubset</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt id="link-141" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.xrefs=obitools.obo.parser.OBOTerm-class.html#xrefs"><a title="obitools.obo.parser.OBOTerm.xrefs" class="py-name" href="#" onclick="return doclink('link-141', 'xrefs', 'link-141');">xrefs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-142" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getXref()=obitools.obo.parser.OBOTerm-class.html#_getXref"><a title="obitools.obo.parser.OBOTerm._getXref" class="py-name" href="#" onclick="return doclink('link-142', '_getXref', 'link-142');">_getXref</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt id="link-143" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.union_of=obitools.obo.parser.OBOTerm-class.html#union_of"><a title="obitools.obo.parser.OBOTerm.union_of" class="py-name" href="#" onclick="return doclink('link-143', 'union_of', 'link-143');">union_of</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-144" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getUnion()=obitools.obo.parser.OBOTerm-class.html#_getUnion"><a title="obitools.obo.parser.OBOTerm._getUnion" class="py-name" href="#" onclick="return doclink('link-144', '_getUnion', 'link-144');">_getUnion</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt id="link-145" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.intersection_of=obitools.obo.parser.OBOTerm-class.html#intersection_of"><a title="obitools.obo.parser.OBOTerm.intersection_of" class="py-name" href="#" onclick="return doclink('link-145', 'intersection_of', 'link-145');">intersection_of</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-146" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getIntersection()=obitools.obo.parser.OBOTerm-class.html#_getIntersection"><a title="obitools.obo.parser.OBOTerm._getIntersection" class="py-name" href="#" onclick="return doclink('link-146', '_getIntersection', 'link-146');">_getIntersection</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt id="link-147" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.disjoint_from=obitools.obo.parser.OBOTerm-class.html#disjoint_from"><a title="obitools.obo.parser.OBOTerm.disjoint_from" class="py-name" href="#" onclick="return doclink('link-147', 'disjoint_from', 'link-147');">disjoint_from</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-148" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getDisjonction()=obitools.obo.parser.OBOTerm-class.html#_getDisjonction"><a title="obitools.obo.parser.OBOTerm._getDisjonction" class="py-name" href="#" onclick="return doclink('link-148', '_getDisjonction', 'link-148');">_getDisjonction</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt id="link-149" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.is_obsolete=obitools.obo.parser.OBOTerm-class.html#is_obsolete"><a title="obitools.obo.parser.OBOTerm.is_obsolete" class="py-name" href="#" onclick="return doclink('link-149', 'is_obsolete', 'link-149');">is_obsolete</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="obitools.obo.parser.OBOTerm._isObsolete" class="py-name" href="#" onclick="return doclink('link-150', '_isObsolete', 'link-112');">_isObsolete</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt id="link-151" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.replace_by=obitools.obo.parser.OBOTerm-class.html#replace_by"><a title="obitools.obo.parser.OBOTerm.replace_by" class="py-name" href="#" onclick="return doclink('link-151', 'replace_by', 'link-151');">replace_by</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-152" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getReplaceBy()=obitools.obo.parser.OBOTerm-class.html#_getReplaceBy"><a title="obitools.obo.parser.OBOTerm._getReplaceBy" class="py-name" href="#" onclick="return doclink('link-152', '_getReplaceBy', 'link-152');">_getReplaceBy</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt id="link-153" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.consider=obitools.obo.parser.OBOTerm-class.html#consider"><a title="obitools.obo.parser.OBOTerm.consider" class="py-name" href="#" onclick="return doclink('link-153', 'consider', 'link-153');">consider</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-154" class="py-name" targets="Method obitools.obo.parser.OBOTerm._getConsider()=obitools.obo.parser.OBOTerm-class.html#_getConsider"><a title="obitools.obo.parser.OBOTerm._getConsider" class="py-name" href="#" onclick="return doclink('link-154', '_getConsider', 'link-154');">_getConsider</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> </tt>
|
|
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOEntryFactory"></a><div id="OBOEntryFactory-def"><a name="L650"></a><tt class="py-lineno">650</tt> <a class="py-toggle" href="#" id="OBOEntryFactory-toggle" onclick="return toggle('OBOEntryFactory');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#OBOEntryFactory">OBOEntryFactory</a><tt class="py-op">(</tt><tt class="py-param">stanza</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="OBOEntryFactory-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OBOEntryFactory-expanded"><a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"><tt class="py-docstring"> Dispatcher of stanza.</tt> </tt>
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<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"><tt class="py-docstring"> @param stanza: a stanza composed of several lines.</tt> </tt>
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<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"><tt class="py-docstring"> @type stanza: text</tt> </tt>
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<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-docstring"> @return: an C{OBOTerm} | C{OBOEntry} instance</tt> </tt>
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<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-docstring"> @note: The dispatcher treats differently the stanza which are OBO "Term"</tt> </tt>
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<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"><tt class="py-docstring"> and the others.</tt> </tt>
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<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> </tt>
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<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-name">stanzaType</tt> <tt class="py-op">=</tt> <tt id="link-155" class="py-name"><a title="obitools.obo.parser.OBOEntry" class="py-name" href="#" onclick="return doclink('link-155', 'OBOEntry', 'link-106');">OBOEntry</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="obitools.obo.parser.OBOEntry.parseStanzaName" class="py-name" href="#" onclick="return doclink('link-156', 'parseStanzaName', 'link-108');">parseStanzaName</a></tt><tt class="py-op">(</tt><tt class="py-name">stanza</tt><tt class="py-op">)</tt> </tt>
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<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> </tt>
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<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stanzaType</tt><tt class="py-op">==</tt><tt class="py-string">"Term"</tt><tt class="py-op">:</tt> </tt>
|
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<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-157" class="py-name" targets="Class obitools.obo.parser.OBOTerm=obitools.obo.parser.OBOTerm-class.html"><a title="obitools.obo.parser.OBOTerm" class="py-name" href="#" onclick="return doclink('link-157', 'OBOTerm', 'link-157');">OBOTerm</a></tt><tt class="py-op">(</tt><tt class="py-name">stanza</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-158" class="py-name"><a title="obitools.obo.parser.OBOEntry" class="py-name" href="#" onclick="return doclink('link-158', 'OBOEntry', 'link-106');">OBOEntry</a></tt><tt class="py-op">(</tt><tt class="py-name">stanza</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> </tt>
|
|
<a name="OBOEntryIterator"></a><div id="OBOEntryIterator-def"><a name="L670"></a><tt class="py-lineno">670</tt> <a class="py-toggle" href="#" id="OBOEntryIterator-toggle" onclick="return toggle('OBOEntryIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.obo.parser-module.html#OBOEntryIterator">OBOEntryIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="OBOEntryIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OBOEntryIterator-expanded"><a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt id="link-159" class="py-name" targets="Function obitools.obo.parser.stanzaIterator()=obitools.obo.parser-module.html#stanzaIterator"><a title="obitools.obo.parser.stanzaIterator" class="py-name" href="#" onclick="return doclink('link-159', 'stanzaIterator', 'link-159');">stanzaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">e</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entries</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">e</tt> </tt>
|
|
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-160" class="py-name" targets="Function obitools.obo.parser.OBOEntryFactory()=obitools.obo.parser-module.html#OBOEntryFactory"><a title="obitools.obo.parser.OBOEntryFactory" class="py-name" href="#" onclick="return doclink('link-160', 'OBOEntryFactory', 'link-160');">OBOEntryFactory</a></tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> </tt><script type="text/javascript">
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