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<a href="Bio-module.html">Package Bio</a> ::
Package Restriction
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<h1 class="epydoc">Source Code for <a href="Bio.Restriction-module.html">Package Bio.Restriction</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Restriction Analysis Libraries.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright (C) 2004. Frederic Sohm.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Usage :</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">=====</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Rana.fts import fts # </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Rana.Vector import * # Just a way to get a sequence.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Seq import Seq # Use your prefer method here.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> >>> pbr = fts(pBR322) #</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> >>> seq = Seq(str(pbr)) #</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> >>></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Restriction import *</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> >>> a = Analysis(AllEnzymes, seq, linear=False)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> >>> b = a.blunt()</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> >>> a.print_that() # no argument -> print all the results</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> AasI : 2169, 2582.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> AatII : 4289.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> Acc16I : 263, 1359, 1457, 3589.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> More enzymes here.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> >>> b = a.without_site()</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> >>> a.print_that(b, '', '\n Enzymes which do not cut pBR322.\n\n')</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> Enzymes which do not cut pBR322.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> AarI AatI Acc65I AcsI AcvI AdeI AflII AgeI </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> AhlI AleI AloI ApaI ApoI AscI AsiAI AsiSI </tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> Asp718I AspA2I AsuII AvaIII AvrII AxyI BaeI BbrPI </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> BbvCI BclI BcuI BfrBI BfrI BglII BlnI BlpI </tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> BmgBI BmgI BplI Bpu1102I Bpu14I BsaXI Bse21I BsePI </tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> BseRI BshTI BsiWI Bsp119I Bsp120I Bsp1407I Bsp1720I Bsp19I </tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> BspT104I BspTI BsrGI BssHI BssHII Bst98I BstAUI BstBI </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> BstEII BstPI BstSNI BstXI Bsu36I BtrI CciNI CelII </tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> Cfr42I Cfr9I CpoI Csp45I CspAI CspCI CspI DraIII </tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> DrdII Ecl136II Eco105I Eco147I Eco72I Eco81I Eco91I EcoICRI </tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> EcoO65I EcoRI EcoT22I EspI FalI FbaI FseI FunII </tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> HpaI KpnI Ksp22I KspAI KspI MabI MfeI MluI </tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> Mph1103I MspCI MssI MunI NcoI NotI NsiI NspV </tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> OliI PacI PaeR7I PasI PauI PceI Pfl23II PinAI </tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> PmaCI PmeI PmlI Ppu10I PsiI Psp124BI PspAI PspCI </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> PspEI PspLI PspOMI PspXI PsrI RleAI Rsr2I RsrII </tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> SacI SacII SanDI SauI SbfI SciI SdaI SexAI </tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> SfiI Sfr274I Sfr303I SfuI SgfI SgrBI SlaI SmaI </tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> SmiI SnaBI SpeI SplI SrfI Sse232I Sse8387I Sse8647I </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> SseBI SspBI SstI StuI SunI SwaI TliI UthSI </tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> Vha464I XapI XbaI XcmI XhoI XmaCI XmaI XmaJI </tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> Zsp2I </tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> >>></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Restriction=Bio.Restriction-module.html,Module Bio.Restriction.Restriction=Bio.Restriction.Restriction-module.html"><a title="Bio.Restriction
Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-1', 'Restriction', 'link-1');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name"><a title="Bio.Restriction
Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-2', 'Restriction', 'link-1');">Restriction</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># OK can't put the following code in Bio.Restriction.__init__ unless</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># I put everything from Restriction in here.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># or at least the RestrictionBatch class.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The reason for that is if I do that, I break the __contains__ method of</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the RestrictionBatch in Restriction, which expect to find the name of</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the enzymes in the locals() dictionary when evaluating string to see if</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># it is an enzyme.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This call for some explanations I guess :</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># When testing for the presence of a Restriction enzyme in a</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># RestrictionBatch, the user can use :</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 1) a class of type 'RestrictionType'</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 2) a string of the name of the enzyme (it's repr)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># i.e :</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> from Bio.Restriction import RestrictionBatch, EcoRI</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> MyBatch = RestrictionBatch(EcoRI)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> #!/usr/bin/env python</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> EcoRI in MyBatch # the class EcoRI.</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># True</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> 'EcoRI' in MyBatch # a string representation</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># True</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># OK, that's how it is suppose to work. And I find it quite useful.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Now if I leave the code here I got :</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> from Bio.Restriction import RestrictionBatch, EcoRI</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> MyBatch = RestrictionBatch(EcoRI)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> EcoRI in MyBatch # the class EcoRI.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># True</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> 'EcoRI' in MyBatch # a string.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># False</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-comment"># There is 5 ways to change that :</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 1) abandon the evaluation of string representation.</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 2) leave the code like that and hack something in RestrictionBatch.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 3) Move back the code in Bio.Restriction.Restriction</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 4) Move RestrictionBatch here.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 5) Remove Restriction.Restriction and move all the code in here</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 1) no fun in that.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 2) there is a simpler way to do it.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 3) I prefer to keep all the code together.</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 4) and 5) both are OK. Only a matter of preference.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># So the following code has been moved back to Bio.Restricion.Restriction</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># For the user the results is transparent:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># from Bio.Restriction import * works as before.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment">###</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### The restriction enzyme classes are created dynamically when the module is</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### imported. Here is the magic which allow the creation of the</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### restriction-enzyme classes.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### The reason for the two dictionaries in Restriction_Dictionary</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### one for the types (which will be called pseudo-type as they really</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### correspond to the values that instances of RestrictionType can take)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### and one for the enzymes is efficiency as the bases are evaluated</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### once per pseudo-type.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### However Restriction is still a very inefficient module at import. But</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### remember that around 660 classes (which is more or less the size of Rebase)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### have to be created dynamically. However, this processing take place only</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### once.</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### This inefficiency is however largely compensated by the use of metaclass</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### which provide a very efficient layout for the class themselves mostly</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### alleviating the need of if/else loops in the class methods.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### It is essential to run Restriction with doc string optimisation (-OO switch)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### as the doc string of 660 classes take a lot of processing.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##CommOnly = RestrictionBatch() # commercial enzymes</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##NonComm = RestrictionBatch() # not available commercially</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##for TYPE, (bases, enzymes) in typedict.iteritems() :</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # The keys are the pseudo-types TYPE (stored as type1, type2...)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # The names are not important and are only present to differentiate</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # the keys in the dict. All the pseudo-types are in fact RestrictionType.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # These names will not be used after and the pseudo-types are not</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # kept in the locals() dictionary. It is therefore impossible to</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # import them.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # Now, if you have look at the dictionary, you will see that not all the</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # types are present as those without corresponding enzymes have been</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # removed by Dictionary_Builder().</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # The values are tuples which contain</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # as first element a tuple of bases (as string) and</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # as second element the names of the enzymes.</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # First eval the bases.</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## bases = tuple([eval(x) for x in bases])</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # now create the particular value of RestrictionType for the classes</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # in enzymes.</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## T = type.__new__(RestrictionType, 'RestrictionType', bases, {})</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## for k in enzymes :</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # Now, we go through all the enzymes and assign them their type.</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # enzymedict[k] contains the values of the attributes for this</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # particular class (self.site, self.ovhg,....).</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## newenz = T(k, bases, enzymedict[k])</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # we add the enzymes to the corresponding batch.</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # No need to verify the enzyme is a RestrictionType -> add_nocheck</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## #</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if newenz.is_comm() : CommOnly.add_nocheck(newenz)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else : NonComm.add_nocheck(newenz)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### AllEnzymes is a RestrictionBatch with all the enzymes from Rebase.</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##AllEnzymes = CommOnly | NonComm</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### Now, place the enzymes in locals so they can be imported.</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##names = [str(x) for x in AllEnzymes]</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##locals().update(dict(map(None, names, AllEnzymes)))</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### Limit what can be imported by from Restriction import *</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### Most of the classes here will never be used outside this module</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### (Defined,Palindromic...). It is still possible to request them specifically</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### also delete the variable that are no longer needed.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### </tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##__all__=['Analysis', 'RestrictionBatch','AllEnzymes','CommOnly','NonComm']+names</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##del k, x, enzymes, TYPE, bases, names</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
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