<?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.Entrez</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> ::
Package Entrez
</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.Entrez-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package Entrez</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Entrez-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Provides code to access NCBI over the WWW.
The main Entrez web page is available at:
http://www.ncbi.nlm.nih.gov/Entrez/
A list of the Entrez utilities is available at:
http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
Functions:
efetch Retrieves records in the requested format from a list of one or
more primary IDs or from the user's environment
epost Posts a file containing a list of primary IDs for future use in
the user's environment to use with subsequent search strategies
esearch Searches and retrieves primary IDs (for use in EFetch, ELink,
and ESummary) and term translations and optionally retains
results for future use in the user's environment.
elink Checks for the existence of an external or Related Articles link
from a list of one or more primary IDs. Retrieves primary IDs
and relevancy scores for links to Entrez databases or Related
Articles; creates a hyperlink to the primary LinkOut provider
for a specific ID and database, or lists LinkOut URLs
and Attributes for multiple IDs.
einfo Provides field index term counts, last update, and available
links for each database.
esummary Retrieves document summaries from a list of primary IDs or from
the user's environment.
egquery Provides Entrez database counts in XML for a single search
using Global Query.
espell Retrieves spelling suggestions.
read Parses the XML results returned by any of the above functions.
Typical usage is:
>>> handle = Entrez.einfo() # or esearch, efetch, ...
>>> record = Entrez.read(handle)
where record is now a Python dictionary or list.
_open Internally used function.
</pre>
<!-- ==================== SUBMODULES ==================== -->
<a name="section-Submodules"></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">Submodules</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Submodules"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr><td class="summary">
<ul class="nomargin">
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser-module.html">Bio.Entrez.Parser</a></strong>: <em class="summary">Parser for XML results returned by NCBI's Entrez Utilities.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Entrez.SerialSet-module.html">Bio.Entrez.SerialSet</a></strong> </li>
</ul></td></tr>
</table>
<br />
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></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">Functions</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Functions"
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.Entrez-module.html#query" class="summary-sig-name">query</a>(<span class="summary-sig-arg">cmd</span>,
<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/sites/entrez</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Query Entrez and return a handle to the HTML results (DEPRECATED).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#query">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.Entrez-module.html#epost" class="summary-sig-name">epost</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Post a file of identifiers for future use.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#epost">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.Entrez-module.html#efetch" class="summary-sig-name">efetch</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Fetches Entrez results which are returned as a handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#efetch">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.Entrez-module.html#esearch" class="summary-sig-name">esearch</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">term</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
ESearch runs an Entrez search and returns a handle to the results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#esearch">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.Entrez-module.html#elink" class="summary-sig-name">elink</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
ELink checks for linked external articles and returns a handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#elink">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.Entrez-module.html#einfo" class="summary-sig-name">einfo</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
EInfo returns a summary of the Entez databases as a results handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#einfo">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.Entrez-module.html#esummary" class="summary-sig-name">esummary</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
ESummary retrieves document summaries as a results handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#esummary">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.Entrez-module.html#egquery" class="summary-sig-name">egquery</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
EGQuery provides Entrez database counts for a global search.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#egquery">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.Entrez-module.html#espell" class="summary-sig-name">espell</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
ESpell retrieves spelling suggestions, returned in a results handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#espell">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.Entrez-module.html#read" class="summary-sig-name">read</a>(<span class="summary-sig-arg">handle</span>)</span><br />
Parses an XML file from the NCBI Entrez Utilities into python
objects.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#read">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.Entrez-module.html#_open" class="summary-sig-name" onclick="show_private();">_open</a>(<span class="summary-sig-arg">cgi</span>,
<span class="summary-sig-arg">params</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span><br />
Helper function to build the URL and open a handle to it (PRIVATE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Entrez-pysrc.html#_open">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></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">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="query"></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">query</span>(<span class="sig-arg">cmd</span>,
<span class="sig-arg">db</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/sites/entrez</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#query">source code</a></span>
</td>
</tr></table>
<p>Query Entrez and return a handle to the HTML results (DEPRECATED).</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp</p>
<p>Return a handle to the results.</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="epost"></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">epost</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#epost">source code</a></span>
</td>
</tr></table>
<p>Post a file of identifiers for future use.</p>
<p>Posts a file containing a list of UIs for future use in the user's
environment to use with subsequent search strategies.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html</p>
<p>Return a handle to the results.</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="efetch"></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">efetch</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#efetch">source code</a></span>
</td>
</tr></table>
<p>Fetches Entrez results which are returned as a handle.</p>
<p>EFetch retrieves records in the requested format from a list of one or
more UIs or from user's environment.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html</p>
<p>Return a handle to the results.</p>
<p>Raises an IOError exception if there's a network error.</p>
<p>Short example:</p>
<p>from Bio import Entrez handle =
Entrez.efetch(db="nucleotide", id="57240072",
rettype="genbank") print handle.read()</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="esearch"></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">esearch</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">term</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#esearch">source code</a></span>
</td>
</tr></table>
<p>ESearch runs an Entrez search and returns a handle to the results.</p>
<p>ESearch searches and retrieves primary IDs (for use in EFetch, ELink
and ESummary) and term translations, and optionally retains results for
future use in the user's environment.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html</p>
<p>Return a handle to the results which are always in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<p>Short example:</p>
<p>from Bio import Entez handle =
Entrez.esearch(db="nucleotide", retmax=10,
term="Opuntia") record = Entrez.read(handle) print
record["Count"] print record["IdList"]</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="elink"></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">elink</span>(<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#elink">source code</a></span>
</td>
</tr></table>
<p>ELink checks for linked external articles and returns a handle.</p>
<p>ELink checks for the existence of an external or Related Articles link
from a list of one or more primary IDs; retrieves IDs and relevancy
scores for links to Entrez databases or Related Articles; creates a
hyperlink to the primary LinkOut provider for a specific ID and database,
or lists LinkOut URLs and attributes for multiple IDs.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html</p>
<p>Return a handle to the results, by default in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="einfo"></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">einfo</span>(<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#einfo">source code</a></span>
</td>
</tr></table>
<p>EInfo returns a summary of the Entez databases as a results
handle.</p>
<p>EInfo provides field names, index term counts, last update, and
available links for each Entrez database.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html</p>
<p>Return a handle to the results, by default in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<p>Short example:</p>
<p>from Bio import Entrez record = Entrez.read(Entrez.einfo()) print
record['DbList']</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="esummary"></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">esummary</span>(<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#esummary">source code</a></span>
</td>
</tr></table>
<p>ESummary retrieves document summaries as a results handle.</p>
<p>ESummary retrieves document summaries from a list of primary IDs or
from the user's environment.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html</p>
<p>Return a handle to the results, by default in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="egquery"></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">egquery</span>(<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#egquery">source code</a></span>
</td>
</tr></table>
<p>EGQuery provides Entrez database counts for a global search.</p>
<p>EGQuery provides Entrez database counts in XML for a single search
using Global Query.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html</p>
<p>Return a handle to the results in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="espell"></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">espell</span>(<span class="sig-arg">cgi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#espell">source code</a></span>
</td>
</tr></table>
<p>ESpell retrieves spelling suggestions, returned in a results
handle.</p>
<p>ESpell retrieves spelling suggestions, if available.</p>
<p>See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html</p>
<p>Return a handle to the results, by default in XML format.</p>
<p>Raises an IOError exception if there's a network error.</p>
<p>Short example:</p>
<p>from Bio import Entrez record =
Entrez.read(Entrez.espell(term="biopythooon")) print
record["Query"] print record["CorrectedQuery"]</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="read"></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">read</span>(<span class="sig-arg">handle</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#read">source code</a></span>
</td>
</tr></table>
<p>Parses an XML file from the NCBI Entrez Utilities into python
objects.</p>
<p>This function parses an XML file created by NCBI's Entrez Utilities,
returning a multilevel data structure of Python lists and dictionaries.
Most XML files returned by NCBI's Entrez Utilities can be parsed by this
function, provided its DTD is available. Biopython includes the DTDs for
most commonly used Entrez Utilities.</p>
<p>Whereas the data structure seems to consist of generic Python lists,
dictionaries, strings, and so on, each of these is actually a class
derived from the base type. This allows us to store the attributes (if
any) of each element in a dictionary my_element.attributes, and the tag
name in my_element.tag.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_open"></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">_open</span>(<span class="sig-arg">cgi</span>,
<span class="sig-arg">params</span>=<span class="sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Entrez-pysrc.html#_open">source code</a></span>
</td>
</tr></table>
<p>Helper function to build the URL and open a handle to it
(PRIVATE).</p>
<p>Open a handle to Entrez. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. Does some simple
error checking, and will raise an IOError if it encounters one.</p>
<p>This function also enforces the "three second rule" to avoid
abusing the NCBI servers.</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>
<!-- 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 09:26:23 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>
