<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.GenBank.utils.FeatureValueCleaner</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.GenBank-module.html">Package GenBank</a> :: <a href="Bio.GenBank.utils-module.html">Module utils</a> :: Class FeatureValueCleaner </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.GenBank.utils.FeatureValueCleaner-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FeatureValueCleaner</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.utils-pysrc.html#FeatureValueCleaner">source code</a></span></p> <pre class="literalblock"> Provide specialized capabilities for cleaning up values in features. This class is designed to provide a mechanism to clean up and process values in the key/value pairs of GenBank features. This is useful because in cases like: /translation="MED YDPWNLRFQSKYKSRDA" you'll end up with a value with s and spaces in it like: "MED YDPWEL..." which you probably don't want. This cleaning needs to be done on a case by case basis since it is impossible to interpret whether you should be concatenating everything (as in translations), or combining things with spaces (as might be the case with /notes). </pre> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">to_process</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">translation</code><code class="variable-quote">'</code><code class="variable-group">]</code></span>)</span><br /> Initialize with the keys we should deal with.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.utils-pysrc.html#FeatureValueCleaner.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.GenBank.utils.FeatureValueCleaner-class.html#clean_value" class="summary-sig-name">clean_value</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">key_name</span>, <span class="summary-sig-arg">value</span>)</span><br /> Clean the specified value and return it.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.utils-pysrc.html#FeatureValueCleaner.clean_value">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_clean_translation"></a><span class="summary-sig-name">_clean_translation</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">value</span>)</span><br /> Concatenate a translation value to one long protein string.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GenBank.utils-pysrc.html#FeatureValueCleaner._clean_translation">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== CLASS VARIABLES ==================== --> <a name="section-ClassVariables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Class Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassVariables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="keys_to_process"></a><span class="summary-name">keys_to_process</span> = <code title="['translation']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">translation</code><code class="variable-quote">'</code><code class="variable-group">]</code></code> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="clean_value"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">clean_value</span>(<span class="sig-arg">self</span>, <span class="sig-arg">key_name</span>, <span class="sig-arg">value</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GenBank.utils-pysrc.html#FeatureValueCleaner.clean_value">source code</a></span> </td> </tr></table> <p>Clean the specified value and return it.</p> <p>If the value is not specified to be dealt with, the original value will be returned.</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- 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