<?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.Scanner.InsdcScanner</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.Scanner-module.html">Module Scanner</a> ::
Class InsdcScanner
</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.Scanner.InsdcScanner-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class InsdcScanner</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner">source code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.GenBank.Scanner.EmblScanner-class.html">EmblScanner</a></li><li>, <a href="Bio.GenBank.Scanner.GenBankScanner-class.html">GenBankScanner</a></li> </ul>
</dd></dl>
<hr />
<p>Basic functions for breaking up a GenBank/EMBL file into sub
sections.</p>
<p>The International Nucleotide Sequence Database Collaboration (INSDC)
between the DDBJ, EMBL, and GenBank. These organisations all use the
same "Feature Table" layout in their plain text flat file
formats.</p>
<p>However, the header and sequence sections of an EMBL file are very
different in layout to those produced by GenBank/DDBJ.</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 name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">debug</span>=<span class="summary-sig-default">0</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.__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 name="set_handle"></a><span class="summary-sig-name">set_handle</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.set_handle">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.Scanner.InsdcScanner-class.html#find_start" class="summary-sig-name">find_start</a>(<span class="summary-sig-arg">self</span>)</span><br />
Read in lines until find the ID/LOCUS line, which is returned.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.find_start">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.Scanner.InsdcScanner-class.html#parse_header" class="summary-sig-name">parse_header</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return list of strings making up the header</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_header">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.Scanner.InsdcScanner-class.html#parse_features" class="summary-sig-name">parse_features</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">skip</span>=<span class="summary-sig-default">False</span>)</span><br />
Return list of tuples for the features (if present)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_features">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.Scanner.InsdcScanner-class.html#parse_feature" class="summary-sig-name">parse_feature</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature_key</span>,
<span class="summary-sig-arg">lines</span>)</span><br />
Expects a feature as a list of strings, returns a tuple (key, location, qualifiers)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_feature">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 name="parse_footer"></a><span class="summary-sig-name">parse_footer</span>(<span class="summary-sig-arg">self</span>)</span><br />
returns a tuple containing a list of any misc strings, and the
sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_footer">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 href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_first_line" class="summary-sig-name" onclick="show_private();">_feed_first_line</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">line</span>)</span><br />
Handle the LOCUS/ID line, passing data to the comsumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_first_line">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 href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_header_lines" class="summary-sig-name" onclick="show_private();">_feed_header_lines</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">lines</span>)</span><br />
Handle the header lines (list of strings), passing data to the
comsumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_header_lines">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 href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_feature_table" class="summary-sig-name" onclick="show_private();">_feed_feature_table</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">feature_tuples</span>)</span><br />
Handle the feature table (list of tuples), passing data to the
comsumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_feature_table">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 href="Bio.GenBank.Scanner.InsdcScanner-class.html#_feed_misc_lines" class="summary-sig-name" onclick="show_private();">_feed_misc_lines</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">lines</span>)</span><br />
Handle any lines between features and sequence (list of strings),
passing data to the consumer</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_misc_lines">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.Scanner.InsdcScanner-class.html#feed" class="summary-sig-name">feed</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">consumer</span>,
<span class="summary-sig-arg">do_features</span>=<span class="summary-sig-default">True</span>)</span><br />
Feed a set of data into the consumer.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.feed">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.Scanner.InsdcScanner-class.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">do_features</span>=<span class="summary-sig-default">True</span>)</span><br />
Returns a SeqRecord (with SeqFeatures if do_features=True)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse">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.Scanner.InsdcScanner-class.html#parse_records" class="summary-sig-name">parse_records</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">do_features</span>=<span class="summary-sig-default">True</span>)</span><br />
Returns a SeqRecord object iterator</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_records">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.Scanner.InsdcScanner-class.html#parse_cds_features" class="summary-sig-name">parse_cds_features</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">ProteinAlphabet()</span>,
<span class="summary-sig-arg">tags2id</span>=<span class="summary-sig-default"><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">protein_id</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">locus_tag</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">product</code><code class="variable-quote">'</code><code class="variable-group">)</code></span>)</span><br />
Returns SeqRecord object iterator</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_cds_features">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="RECORD_START"></a><span class="summary-name">RECORD_START</span> = <code title="'XXX'"><code class="variable-quote">'</code><code class="variable-string">XXX</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="HEADER_WIDTH"></a><span class="summary-name">HEADER_WIDTH</span> = <code title="3">3</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_START_MARKERS"></a><span class="summary-name">FEATURE_START_MARKERS</span> = <code title="['XXX***FEATURES***XXX']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">XXX***FEATURES***XXX</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_END_MARKERS"></a><span class="summary-name">FEATURE_END_MARKERS</span> = <code title="['XXX***END FEATURES***XXX']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">XXX***END FEATURES***XXX</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_QUALIFIER_INDENT"></a><span class="summary-name">FEATURE_QUALIFIER_INDENT</span> = <code title="0">0</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_QUALIFIER_SPACER"></a><span class="summary-name">FEATURE_QUALIFIER_SPACER</span> = <code title="''"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="SEQUENCE_HEADERS"></a><span class="summary-name">SEQUENCE_HEADERS</span> = <code title="['XXX']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">XXX</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="find_start"></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">find_start</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.find_start">source code</a></span>
</td>
</tr></table>
<p>Read in lines until find the ID/LOCUS line, which is returned.</p>
<p>Any preamble (such as the header used by the NCBI on *.seq.gz
archives) will we ignored.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse_header"></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">parse_header</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_header">source code</a></span>
</td>
</tr></table>
<p>Return list of strings making up the header</p>
<p>New line characters are removed.</p>
<p>Assumes you have just read in the ID/LOCUS line.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse_features"></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">parse_features</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">skip</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_features">source code</a></span>
</td>
</tr></table>
<p>Return list of tuples for the features (if present)</p>
<p>Each feature is returned as a tuple (key, location, qualifiers) where
key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers is
a list of two string tuples (feature qualifier keys and values).</p>
<p>Assumes you have already read to the start of the features table.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse_feature"></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">parse_feature</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature_key</span>,
<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_feature">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Expects a feature as a list of strings, returns a tuple (key, location, qualifiers)
For example given this GenBank feature:
CDS complement(join(490883..490885,1..879))
/locus_tag="NEQ001"
/note="conserved hypothetical [Methanococcus jannaschii];
COG1583:Uncharacterized ACR; IPR001472:Bipartite nuclear
localization signal; IPR002743: Protein of unknown
function DUF57"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="NP_963295.1"
/db_xref="GI:41614797"
/db_xref="GeneID:2732620"
/translation="MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK
EKYFNFTLIPKKDIIENKRYYLIISSPDKRFIEVLHNKIKDLDIITIGLAQFQLRKTK
KFDPKLRFPWVTITPIVLREGKIVILKGDKYYKVFVKRLEELKKYNLIKKKEPILEEP
IEISLNQIKDGWKIIDVKDRYYDFRNKSFSAFSNWLRDLKEQSLRKYNNFCGKNFYFE
EAIFEGFTFYKTVSIRIRINRGEAVYIGTLWKELNVYRKLDKEEREFYKFLYDCGLGS
LNSMGFGFVNTKKNSAR"
Then should give input key="CDS" and the rest of the data as a list of strings
lines=["complement(join(490883..490885,1..879))", ..., "LNSMGFGFVNTKKNSAR"]
where the leading spaces and trailing newlines have been removed.
Returns tuple containing: (key as string, location string, qualifiers as list)
as follows for this example:
key = "CDS", string
location = "complement(join(490883..490885,1..879))", string
qualifiers = list of string tuples:
[('locus_tag', '"NEQ001"'),
('note', '"conserved hypothetical [Methanococcus jannaschii];
COG1583:..."'),
('codon_start', '1'),
('transl_table', '11'),
('product', '"hypothetical protein"'),
('protein_id', '"NP_963295.1"'),
('db_xref', '"GI:41614797"'),
('db_xref', '"GeneID:2732620"'),
('translation', '"MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK
EKYFNFT..."')]
In the above example, the "note" and "translation" were edited for compactness,
and they would contain multiple new line characters (displayed above as
)
If a qualifier is quoted (in this case, everything except codon_start and
transl_table) then the quotes are NOT removed.
Note that no whitespace is removed.
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_feed_first_line"></a>
<div class="private">
<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">_feed_first_line</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">line</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_first_line">source code</a></span>
</td>
</tr></table>
<p>Handle the LOCUS/ID line, passing data to the comsumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_feed_header_lines"></a>
<div class="private">
<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">_feed_header_lines</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_header_lines">source code</a></span>
</td>
</tr></table>
<p>Handle the header lines (list of strings), passing data to the
comsumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_feed_feature_table"></a>
<div class="private">
<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">_feed_feature_table</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">feature_tuples</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_feature_table">source code</a></span>
</td>
</tr></table>
<p>Handle the feature table (list of tuples), passing data to the
comsumer</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_feed_misc_lines"></a>
<div class="private">
<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">_feed_misc_lines</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner._feed_misc_lines">source code</a></span>
</td>
</tr></table>
<p>Handle any lines between features and sequence (list of strings),
passing data to the consumer</p>
<p>This should be implemented by the EMBL / GenBank specific subclass</p>
<p>Used by the parse_records() and parse() methods.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="feed"></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">feed</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">handle</span>,
<span class="sig-arg">consumer</span>,
<span class="sig-arg">do_features</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.feed">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Feed a set of data into the consumer.
This method is intended for use with the "old" code in Bio.GenBank
Arguments:
handle - A handle with the information to parse.
consumer - The consumer that should be informed of events.
do_features - Boolean, should the features be parsed?
Skipping the features can be much faster.
Return values:
true - Passed a record
false - Did not find a record
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse"></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">parse</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">handle</span>,
<span class="sig-arg">do_features</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse">source code</a></span>
</td>
</tr></table>
<p>Returns a SeqRecord (with SeqFeatures if do_features=True)</p>
<p>See also the method parse_records() for use on multi-record files.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse_records"></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">parse_records</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">handle</span>,
<span class="sig-arg">do_features</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_records">source code</a></span>
</td>
</tr></table>
<p>Returns a SeqRecord object iterator</p>
<p>Each record (from the ID/LOCUS line to the // line) becomes a
SeqRecord</p>
<p>The SeqRecord objects include SeqFeatures if do_features=True</p>
<p>This method is intended for use in Bio.SeqIO</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="parse_cds_features"></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">parse_cds_features</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">handle</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">ProteinAlphabet()</span>,
<span class="sig-arg">tags2id</span>=<span class="sig-default"><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">protein_id</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">locus_tag</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">product</code><code class="variable-quote">'</code><code class="variable-group">)</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Scanner-pysrc.html#InsdcScanner.parse_cds_features">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Returns SeqRecord object iterator
Each CDS feature becomes a SeqRecord.
alphabet - Used for any sequence found in a translation field.
tags2id - Tupple of three strings, the feature keys to use
for the record id, name and description,
This method is intended for use in Bio.SeqIO
</pre>
<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>
<!-- 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 09:26:34 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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
