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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module ReseekFile
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.ReseekFile-module.html">Module Bio.EUtils.ReseekFile</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Wrap a file handle to allow seeks back to the beginning</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Sometimes data coming from a socket or other input file handle isn't</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">what it was supposed to be. For example, suppose you are reading from</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">a buggy server which is supposed to return an XML stream but can also</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">return an unformatted error message. (This often happens because the</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">server doesn't handle incorrect input very well.)</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">A ReseekFile helps solve this problem. It is a wrapper to the</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">original input stream but provides a buffer. Read requests to the</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">ReseekFile get forwarded to the input stream, appended to a buffer,</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">then returned to the caller. The buffer contains all the data read so</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">far.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">The ReseekFile can be told to reseek to the start position. The next</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">read request will come from the buffer, until the buffer has been</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">read, in which case it gets the data from the input stream. This</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">newly read data is also appended to the buffer.</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">When buffering is no longer needed, use the 'nobuffer()' method. This</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">tells the ReseekFile that once it has read from the buffer it should</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">throw the buffer away. After nobuffer is called, the behaviour of</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">'seek' is no longer defined.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">For example, suppose you have the server as above which either</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">gives an error message is of the form:</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"> ERROR: cannot do that</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">or an XML data stream, starting with "<?xml".</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> infile = urllib2.urlopen("http://somewhere/")</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> infile = ReseekFile.ReseekFile(infile)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> s = infile.readline()</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> if s.startswith("ERROR:"):</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> raise Exception(s[:-1])</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> infile.seek(0)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> infile.nobuffer() # Don't buffer the data</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> ... process the XML from infile ...</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring">This module also implements 'prepare_input_source(source)' modeled on</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring">xml.sax.saxutils.prepare_input_source. This opens a URL and if the</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">input stream is not already seekable, wraps it in a ReseekFile.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">NOTE:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> Don't use bound methods for the ReseekFile. When the buffer is</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">empty, the ReseekFile reassigns the input file's read/readlines/etc.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">method as instance variable. This gives slightly better performance</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring">at the cost of not allowing an infrequently used idiom.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> Use tell() to get the beginning byte location. ReseekFile will</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring">attempt to get the real position from the wrapped file and use that as</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring">the beginning location. If the wrapped file does not support tell(),</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring">ReseekFile.tell() will return 0.</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"> readlines does not yet support a sizehint. Want to</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring">an implementation?</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring">The latest version of this code can be found at</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> http://www.dalkescientific.com/Python/</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"># Written in 2003 by Andrew Dalke, Dalke Scientific Software, LLC.</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"># This software has been released to the public domain. No</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"># copyright is asserted.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="ReseekFile"></a><div id="ReseekFile-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="ReseekFile-toggle" onclick="return toggle('ReseekFile');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html">ReseekFile</a><tt class="py-op">:</tt> </tt>
</div><div id="ReseekFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ReseekFile-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""wrap a file handle to allow seeks back to the beginning</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> Takes a file handle in the constructor.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> See the module docstring for more documentation.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ReseekFile.__init__"></a><div id="ReseekFile.__init__-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="ReseekFile.__init__-toggle" onclick="return toggle('ReseekFile.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-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">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReseekFile.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.__init__-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">at_beginning</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beginning</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-0', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-op">(</tt><tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beginning</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_use_buffer</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.seek"></a><div id="ReseekFile.seek-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="ReseekFile.seek-toggle" onclick="return toggle('ReseekFile.seek');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#seek">seek</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">,</tt> <tt class="py-param">whence</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReseekFile.seek-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.seek-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""offset, whence = 0</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> Seek to a given byte position. Only supports whence == 0</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> and offset == the initial value of ReseekFile.tell() (which</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> is usually 0, but not always.)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">whence</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unexpected whence value of %s; expecting 0"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">whence</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">offset</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beginning</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unexpected offset value of %r; expecting '%s'"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">offset</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beginning</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-1', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">at_beginning</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.tell"></a><div id="ReseekFile.tell-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="ReseekFile.tell-toggle" onclick="return toggle('ReseekFile.tell');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#tell">tell</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="ReseekFile.tell-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.tell-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""the current position of the file</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> The initial position may not be 0 if the underlying input</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> file supports tell and it not at position 0.</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <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">at_beginning</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"ReseekFile cannot tell except at the beginning of file"</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beginning</tt> </tt>
</div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="ReseekFile._read"></a><div id="ReseekFile._read-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="ReseekFile._read-toggle" onclick="return toggle('ReseekFile._read');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#_read">_read</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">size</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReseekFile._read-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile._read-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-2" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-2', 'size', 'link-2');">size</a></tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-3', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-4', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">y</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</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">_use_buffer</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-5', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">z</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-6" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-6', 'size', 'link-2');">size</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt id="link-7" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-7', 'x', 'link-7');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-8', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-9', 'size', 'link-2');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-10', 'x', 'link-7');">x</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt id="link-11" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-11', 'size', 'link-2');">size</a></tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-12', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-13', 'size', 'link-2');">size</a></tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-14', 'x', 'link-7');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_use_buffer</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-15', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-16" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-16', 'x', 'link-7');">x</a></tt> <tt class="py-op">+</tt> <tt class="py-name">y</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-17', 'x', 'link-7');">x</a></tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.read"></a><div id="ReseekFile.read-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="ReseekFile.read-toggle" onclick="return toggle('ReseekFile.read');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#read">read</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">size</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>
</div><div id="ReseekFile.read-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.read-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-docstring">"""read up to 'size' bytes from the file</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> Default is -1, which means to read to end of file.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-18', 'x', 'link-7');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile._read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#_read"><a title="Bio.EUtils.ReseekFile.ReseekFile._read" class="py-name" href="#" onclick="return doclink('link-19', '_read', 'link-19');">_read</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-20', 'size', 'link-2');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</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">at_beginning</tt> <tt class="py-keyword">and</tt> <tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-7');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">at_beginning</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile._check_no_buffer()=Bio.EUtils.ReseekFile.ReseekFile-class.html#_check_no_buffer"><a title="Bio.EUtils.ReseekFile.ReseekFile._check_no_buffer" class="py-name" href="#" onclick="return doclink('link-22', '_check_no_buffer', 'link-22');">_check_no_buffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-23" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-23', 'x', 'link-7');">x</a></tt> </tt>
</div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.readline"></a><div id="ReseekFile.readline-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="ReseekFile.readline-toggle" onclick="return toggle('ReseekFile.readline');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#readline">readline</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="ReseekFile.readline-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.readline-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-docstring">"""read a line from the file"""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-comment"># Can we get it out of the buffer_file?</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-24" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-25', 'readline', 'link-25');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-26', 's', 'link-24');">s</a></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-op">==</tt> <tt class="py-string">"\n"</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-24');">s</a></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># No, so now we read a line from the input file</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-28', 'readline', 'link-25');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-comment"># Append the new data to the buffer, if still buffering</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</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">_use_buffer</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-29', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<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 id="link-30" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile._check_no_buffer" class="py-name" href="#" onclick="return doclink('link-30', '_check_no_buffer', 'link-22');">_check_no_buffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-31" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-31', 's', 'link-24');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">t</tt> </tt>
</div><a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.readlines"></a><div id="ReseekFile.readlines-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="ReseekFile.readlines-toggle" onclick="return toggle('ReseekFile.readlines');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines">readlines</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="ReseekFile.readlines-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.readlines-expanded"><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-docstring">"""read all remaining lines from the file"""</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-32', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-33', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-34" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-34');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-35', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-36', 'find', 'link-36');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">j</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="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-38', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-34');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</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="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-40', 'i', 'link-34');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-41', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-42', 'find', 'link-36');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-44', 'i', 'link-34');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-45', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-comment"># Only get here if the last line doesn't have a newline</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-46', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-47', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-34');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">lines</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="ReseekFile._check_no_buffer"></a><div id="ReseekFile._check_no_buffer-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="ReseekFile._check_no_buffer-toggle" onclick="return toggle('ReseekFile._check_no_buffer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#_check_no_buffer">_check_no_buffer</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="ReseekFile._check_no_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile._check_no_buffer-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-comment"># If 'nobuffer' called and finished with the buffer file</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"># then get rid of the buffer and redirect everything to</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"># the original input file.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</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">_use_buffer</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-49', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> \ </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># I'm doing this for the slightly better performance</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-50', 'seek', 'link-1');">seek</a></tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">"seek"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-51', 'tell', 'link-0');">tell</a></tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">"tell"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-52', 'read', 'link-3');">read</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-53', 'read', 'link-3');">read</a></tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-54', 'readline', 'link-25');">readline</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-55', 'readline', 'link-25');">readline</a></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-56', 'readlines', 'link-56');">readlines</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-57', 'readlines', 'link-56');">readlines</a></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">buffer_file</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
<a name="ReseekFile.nobuffer"></a><div id="ReseekFile.nobuffer-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="ReseekFile.nobuffer-toggle" onclick="return toggle('ReseekFile.nobuffer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile.ReseekFile-class.html#nobuffer">nobuffer</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="ReseekFile.nobuffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ReseekFile.nobuffer-expanded"><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-docstring">"""tell the ReseekFile to stop using the buffer once it's exhausted"""</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_use_buffer</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="prepare_input_source"></a><div id="prepare_input_source-def"><a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="prepare_input_source-toggle" onclick="return toggle('prepare_input_source');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile-module.html#prepare_input_source">prepare_input_source</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="prepare_input_source-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="prepare_input_source-expanded"><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-docstring">"""given a URL, returns a xml.sax.xmlreader.InputSource</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> Works like xml.sax.saxutils.prepare_input_source. Wraps the</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> InputSource in a ReseekFile if the URL returns a non-seekable</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> file.</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> To turn the buffer off if that happens, you'll need to do</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> something like</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"> f = source.getCharacterStream()</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> try:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"> f.nobuffer()</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> except AttributeError:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> pass</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> or</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> if isinstance(f, ReseekFile):</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> f.nobuffer()</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">saxutils</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-58" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-58', 'source', 'link-58');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Function Bio.EUtils.ReseekFile.prepare_input_source()=Bio.EUtils.ReseekFile-module.html#prepare_input_source"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-59', 'prepare_input_source', 'link-59');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-60', 'source', 'link-58');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment"># Is this correct? Don't know - don't have Unicode exprerience</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-61', 'source', 'link-58');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-62" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-62', 'source', 'link-58');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-63', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-op">(</tt><tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-name">IOError</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Module Bio.EUtils.ReseekFile=Bio.EUtils.ReseekFile-module.html,Class Bio.EUtils.ReseekFile.ReseekFile=Bio.EUtils.ReseekFile.ReseekFile-class.html"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-64', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-65', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-66', 'source', 'link-58');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">setByteStream</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt id="link-67" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-67', 'source', 'link-58');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">setCharacterStream</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-68" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-68', 'source', 'link-58');">source</a></tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="test_reads"></a><div id="test_reads-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="test_reads-toggle" onclick="return toggle('test_reads');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile-module.html#test_reads">test_reads</a><tt class="py-op">(</tt><tt class="py-param">test_s</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">seek0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_reads-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_reads-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-69', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"Th"</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-70', 'read', 'link-3');">read</a></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">"is "</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-71', 'read', 'link-3');">read</a></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">"is a"</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-72', 'read', 'link-3');">read</a></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="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-73', 'read', 'link-3');">read</a></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="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-74', 'read', 'link-3');">read</a></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">" test."</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-75', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">seek0</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-76', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"Th"</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-77', 'read', 'link-3');">read</a></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">"is "</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-78', 'read', 'link-3');">read</a></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">"is a"</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-79', 'read', 'link-3');">read</a></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="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-80', 'read', 'link-3');">read</a></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="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-81', 'read', 'link-3');">read</a></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">" test."</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-82', 'read', 'link-3');">read</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-string">"\n"</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-83', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"12345"</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-84', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"67890\n"</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-85', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">seek0</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-86', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">test_s</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-87', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">seek0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="test"></a><div id="test-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="test-toggle" onclick="return toggle('test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.ReseekFile-module.html#test">test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test-expanded"><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-88', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"This is a test.\n1234567890\n"</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-89', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-comment"># Test with a normal file</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-90" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-90', 'x', 'link-7');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-91', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt id="link-92" class="py-name" targets="Function Bio.EUtils.ReseekFile.test_reads()=Bio.EUtils.ReseekFile-module.html#test_reads"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-92', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-93', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-94', 'x', 'link-7');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-95', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-96', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">,</tt> <tt id="link-97" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-97', 'x', 'link-7');">x</a></tt><tt class="py-op">)</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"># Test with a ReseekFile wrapper</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-98', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-99', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-100', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt id="link-101" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-101', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-102" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-102', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-103', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-104" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-104', 's', 'link-24');">s</a></tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-105', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-comment"># Make sure the tell offset is correct (may not be 0)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-106" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-106', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-107', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-108" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-108', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-109', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-110', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-111', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-112', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-113', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-114" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-114', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-115', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-116" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-116', 's', 'link-24');">s</a></tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-117', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</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"># Test the ability to turn off buffering and have changes</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># propogate correctly</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-118" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-118', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-119', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-120" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-120', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-121', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">y</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-122', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1000</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">rf</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-123', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.nobuffer()=Bio.EUtils.ReseekFile.ReseekFile-class.html#nobuffer"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-124', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-125', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">y</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt id="link-126" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-126', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-127', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-128', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-129" class="py-name"><a title="Bio.EUtils.ReseekFile.test_reads" class="py-name" href="#" onclick="return doclink('link-129', 'test_reads', 'link-92');">test_reads</a></tt><tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-130', 's', 'link-24');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">,</tt> <tt class="py-name">y</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">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-131', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-132" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-132', 's', 'link-24');">s</a></tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-133', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-comment"># turn off buffering after partial reads</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-134" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-134', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-135', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-136', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-137', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-138', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-139', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-140', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-141', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-142" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-142', 's', 'link-24');">s</a></tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-143" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-143', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-144', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-145" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-145', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-146', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-147', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-148', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-149', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-150', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">t</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-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-151" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-151', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-152', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-153" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-153', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-154', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-155', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt id="link-156" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-156', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-157', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</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">rf</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-158', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-159', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-160" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-160', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"X"</tt> <tt class="py-op">+</tt> <tt id="link-161" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-161', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-162', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-163', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-164', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-165', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt id="link-166" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-166', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-167', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-168', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-169" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-169', 's', 'link-24');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">+</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-comment"># Should only do this test on Unix systems</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-string">"echo HELLO_THERE"</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">infile</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-170', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</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">rf</tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-171', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-172', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-173', 'read', 'link-3');">read</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-string">"E"</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-174', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"LL"</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-175', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-176', 'read', 'link-3');">read</a></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">"ELLO"</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-177', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-178', 'read', 'link-3');">read</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-string">"E"</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-179', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-180', 'read', 'link-3');">read</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-string">"L"</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-181', 'read', 'link-3');">read</a></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">"LO_T"</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-182', 'read', 'link-3');">read</a></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">"HERE"</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-183', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot seek here!"</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-184', 'tell', 'link-0');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot tell here!"</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-comment"># Check if readline/readlines works</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-185" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-185', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"This is line 1.\nAnd line 2.\nAnd now, page 3!"</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-186" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-186', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-187" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-187', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-188', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-189', 'readline', 'link-25');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"his is line 1.\n"</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-190', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-191', 'readline', 'link-25');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"This is line 1.\n"</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-192', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-193', 'readline', 'link-25');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"d line 2.\n"</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-194', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-195', 'readlines', 'link-56');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"This is line 1.\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-string">"And line 2.\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-string">"And now, page 3!"</tt><tt class="py-op">]</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-196', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-197', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-198" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-198', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-199', 'readlines', 'link-56');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">[</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">rf</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-200', 'seek', 'link-1');">seek</a></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>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-comment"># Now there is a final newline</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-201" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-201', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"This is line 1.\nAnd line 2.\nAnd now, page 3!\n"</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">rf</tt> <tt class="py-op">=</tt> <tt id="link-202" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-202', 'ReseekFile', 'link-64');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-203', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-204', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-205', 'seek', 'link-1');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-206', 'nobuffer', 'link-124');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rf</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-207', 'readlines', 'link-56');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"This is line 1.\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-string">"And line 2.\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-string">"And now, page 3!\n"</tt><tt class="py-op">]</tt> </tt>
</div><a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt id="link-208" class="py-name" targets="Function Bio.Decode.test()=Bio.Decode-module.html#test,Function Bio.EUtils.ReseekFile.test()=Bio.EUtils.ReseekFile-module.html#test,Package Martel.test=Martel.test-module.html,Method Martel.test.support.Storage.test()=Martel.test.support.Storage-class.html#test,Function Martel.test.test()=Martel.test-module.html#test,Function Martel.test.test_Expression.test()=Martel.test.test_Expression-module.html#test,Function Martel.test.test_Generate.test()=Martel.test.test_Generate-module.html#test,Function Martel.test.test_IterParser.test()=Martel.test.test_IterParser-module.html#test,Function Martel.test.test_Iterator.test()=Martel.test.test_Iterator-module.html#test,Function Martel.test.test_LAX.test()=Martel.test.test_LAX-module.html#test,Function Martel.test.test_ParseRecords.test()=Martel.test.test_ParseRecords-module.html#test,Function Martel.test.test_Parser.test()=Martel.test.test_Parser-module.html#test,Function Martel.test.test_RecordReader.test()=Martel.test.test_RecordReader-module.html#test,Function Martel.test.test_RecordReader2.test()=Martel.test.test_RecordReader2-module.html#test,Function Martel.test.test_Time.test()=Martel.test.test_Time-module.html#test,Function Martel.test.test_attrs.test()=Martel.test.test_attrs-module.html#test,Function Martel.test.test_convert_re.test()=Martel.test.test_convert_re-module.html#test,Function Martel.test.test_delimiter.test()=Martel.test.test_delimiter-module.html#test,Function Martel.test.test_macros.test()=Martel.test.test_macros-module.html#test,Function Martel.test.test_optimize.test()=Martel.test.test_optimize-module.html#test,Function Martel.test.test_swissprot38.test()=Martel.test.test_swissprot38-module.html#test"><a title="Bio.Decode.test
Bio.EUtils.ReseekFile.test
Martel.test
Martel.test.support.Storage.test
Martel.test.test
Martel.test.test_Expression.test
Martel.test.test_Generate.test
Martel.test.test_IterParser.test
Martel.test.test_Iterator.test
Martel.test.test_LAX.test
Martel.test.test_ParseRecords.test
Martel.test.test_Parser.test
Martel.test.test_RecordReader.test
Martel.test.test_RecordReader2.test
Martel.test.test_Time.test
Martel.test.test_attrs.test
Martel.test.test_convert_re.test
Martel.test.test_delimiter.test
Martel.test.test_macros.test
Martel.test.test_optimize.test
Martel.test.test_swissprot38.test" class="py-name" href="#" onclick="return doclink('link-208', 'test', 'link-208');">test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt><script type="text/javascript">
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