<?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.SeqIO.FastaIO.FastaWriter</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.SeqIO-module.html">Package SeqIO</a> :: <a href="Bio.SeqIO.FastaIO-module.html">Module FastaIO</a> :: Class FastaWriter </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.SeqIO.FastaIO.FastaWriter-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FastaWriter</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.FastaIO-pysrc.html#FastaWriter">source code</a></span></p> <pre class="base-tree"> <a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a> --+ | <a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a> --+ | <strong class="uidshort">FastaWriter</strong> </pre> <hr /> <p>Class to write Fasta format files.</p> <!-- ==================== 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 href="Bio.SeqIO.FastaIO.FastaWriter-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">wrap</span>=<span class="summary-sig-default">60</span>, <span class="summary-sig-arg">record2title</span>=<span class="summary-sig-default">None</span>)</span><br /> Create a Fasta writer.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.FastaIO-pysrc.html#FastaWriter.__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.SeqIO.FastaIO.FastaWriter-class.html#write_record" class="summary-sig-name">write_record</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">record</span>)</span><br /> Write a single Fasta record to the file.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.FastaIO-pysrc.html#FastaWriter.write_record">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a></code></b>: <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_file">write_file</a></code>, <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_footer">write_footer</a></code>, <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_header">write_header</a></code>, <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_records">write_records</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a></code></b>: <code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean">clean</a></code> </p> </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="__init__"></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">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">handle</span>, <span class="sig-arg">wrap</span>=<span class="sig-default">60</span>, <span class="sig-arg">record2title</span>=<span class="sig-default">None</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.FastaIO-pysrc.html#FastaWriter.__init__">source code</a></span> </td> </tr></table> <pre class="literalblock"> Create a Fasta writer. handle - Handle to an output file, e.g. as returned by open(filename, "w") wrap - Optional line length used to wrap sequence lines. Defaults to wrapping the sequence at 60 characters Use zero (or None) for no wrapping, giving a single long line for the sequence. record2title - Optional function to return the text to be used for the title line of each record. By default the a combination of the record.id and record.description is used. If the record.description starts with the record.id, then just the record.description is used. You can either use: myWriter = FastaWriter(open(filename,"w")) writer.write_file(myRecords) Or, follow the sequential file writer system, for example: myWriter = FastaWriter(open(filename,"w")) writer.write_header() # does nothing for Fasta files ... Multiple calls to writer.write_record() and/or writer.write_records() ... writer.write_footer() # does nothing for Fasta files writer.close() </pre> <dl class="fields"> <dt>Overrides: <a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#__init__">Interfaces.SequenceWriter.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="write_record"></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">write_record</span>(<span class="sig-arg">self</span>, <span class="sig-arg">record</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.FastaIO-pysrc.html#FastaWriter.write_record">source code</a></span> </td> </tr></table> <p>Write a single Fasta record to the file.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_record">Interfaces.SequentialSequenceWriter.write_record</a> </dt> </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> <!-- 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 border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:38 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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