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<a href="Bio-module.html">Package Bio</a> ::
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Module DBIdsClient
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module DBIdsClient</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.EUtils.DBIdsClient-pysrc.html">source code</a></span></p>
<p>Search and retrieve information given a set of database
identifiers.</p>
<p>EUtils has two major modes. One uses history while the other uses
database identifiers. This is a high-level interface for working with
identifiers. You should use this module to get information about a set
of known database identifiers.</p>
<p>See HistoryClient if you want to work with a large number of
identifiers or potentially large search results.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio <span class="py-keyword">import</span> EUtils
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.EUtils <span class="py-keyword">import</span> DBIdsClient
<span class="py-prompt">>>> </span>client = DBIdsClient.DBIdsClient()
<span class="py-prompt">>>> </span>result = client.search(<span class="py-string">"dalke"</span>, retmax = 100)
<span class="py-prompt">>>> </span>len(result)
<span class="py-output">30</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> result[0].efetch(retmode = <span class="py-string">"text"</span>, rettype = <span class="py-string">"abstract"</span>).read()</pre>
<p>1: Pac Symp Biocomput 1997;:85-96</p>
<p>Using Tcl for molecular visualization and analysis.</p>
<p>Dalke A, Schulten K.</p>
<p>Beckman Institute, Urbana, IL 61801, USA.</p>
<p>Reading and manipulating molecular structure data is a standard task
in every molecular visualization and analysis program, but is rarely
available in a form readily accessible to the user. Instead, the
development of new methods for analysis, display, and interaction is
often achieved by writing a new program, rather than building on
pre-existing software. We present the Tcl-based script language used in
our molecular modeling program, VMD, and show how it can access
information about the molecular structure, perform analysis, and
graphically display and animate the results. The commands are available
to the user and make VMD a useful environment for studying
biomolecules.</p>
<p>PMID: 9390282 [PubMed - indexed for MEDLINE]</p>
<p>>>></p>
<p>Find sequences similar to GI:4579714 which were published in 2002.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>protein = DBIdsClient.from_dbids(EUtils.DBIds(<span class="py-string">"protein"</span>, <span class="py-string">"4579714"</span>))
<span class="py-prompt">>>> </span>neighbors = protein.neighbor_links(<span class="py-string">"protein"</span>,
<span class="py-more">... </span> daterange = EUtils.DateRange(<span class="py-string">"2002/01/01"</span>, <span class="py-string">"2002/12/31"</span>, <span class="py-string">"pdat"</span>))
<span class="py-prompt">>>> </span>dbids = neighbors.linksetdbs[<span class="py-string">"protein_protein"</span>].dbids
<span class="py-prompt">>>> </span>len(dbids)
<span class="py-output">28</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> dbids
<span class="py-output">DBIds(u'protein', [u'4579714', u'25298947', u'24158913', u'24158914', u'24158915', u'17942993', u'17942994', u'17942995', u'20150921', u'20150922', u'20151159', u'25298949', u'19716034', u'20663737', u'20663738', u'20663741', u'24987328', u'25533128', u'25298946', u'25298948', u'23008597', u'20219020', u'21218340', u'21218344', u'19075395', u'21218338', u'21218342', u'21311795'])</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> client.from_dbids(dbids[:5]).efetch(retmode=<span class="py-string">"text"</span>,
<span class="py-more">... </span> rettype=<span class="py-string">"summary"</span>).read()</pre>
<p>1: BAA75200 Bacteriorhodopsin [Halobacterium sp.]
gi|4579714|dbj|BAA75200.1|[4579714]</p>
<p>2: H84300 bacteriorhodopsin [imported] - Halobacterium sp. NRC-1
gi|25298947|pir||H84300[25298947]</p>
<p>3: 1M0KA Chain A, Bacteriorhodopsin K Intermediate At 1.43 A
Resolution gi|24158913|pdb|1M0K|A[24158913]</p>
<p>4: 1M0LA Chain A, BacteriorhodopsinLIPID COMPLEX AT 1.47 A RESOLUTION
gi|24158914|pdb|1M0L|A[24158914]</p>
<p>5: 1M0MA Chain A, Bacteriorhodopsin M1 Intermediate At 1.43 A
Resolution gi|24158915|pdb|1M0M|A[24158915]</p>
<p>>>></p>
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<a href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html" class="summary-name">DBIdsLookup</a><br />
Look up information about a DBIds
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<a href="Bio.EUtils.DBIdsClient.DBIdsRecord-class.html" class="summary-name">DBIdsRecord</a><br />
A single record on the server
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<a href="Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html" class="summary-name">SequenceDBIdsFetchMixin</a><br />
Support 'efetch' for sequence records
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<a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html" class="summary-name">SequenceDBIdsRecord</a><br />
a single sequence record, referenced by database identifier
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<a href="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html" class="summary-name">PublicationDBIdsFetchMixin</a><br />
Support 'efetch' for publication records
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<a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html" class="summary-name">PublicationDBIdsRecord</a><br />
a single publication record, referenced by database identifier
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<a href="Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html" class="summary-name">BaseDBIdsRecordSet</a><br />
Base class for dealing with a set of records, reference by
identifier
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<a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html" class="summary-name">SequenceDBIdsRecordSet</a><br />
a set of sequence records, referenced by database identifier
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<a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html" class="summary-name">PublicationDBIdsRecordSet</a><br />
a set of publication records, referenced by database identifier
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<a href="Bio.EUtils.DBIdsClient.DBIdsClient-class.html" class="summary-name">DBIdsClient</a><br />
Create a RecordSet either from a search or a set of dbids
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<td><span class="summary-sig"><a name="_get_recordset_constructor"></a><span class="summary-sig-name">_get_recordset_constructor</span>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">dbtype</span>)</span><br />
get the right DataSet constructor for a database</td>
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<td><span class="summary-sig"><a href="Bio.EUtils.DBIdsClient-module.html#from_dbids" class="summary-sig-name">from_dbids</a>(<span class="summary-sig-arg">dbids</span>,
<span class="summary-sig-arg">dbtype</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">eutils</span>=<span class="summary-sig-default">None</span>)</span><br />
create a RecordSet interface for the set of database identifiers</td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">from_dbids</span>(<span class="sig-arg">dbids</span>,
<span class="sig-arg">dbtype</span>=<span class="sig-default">None</span>,
<span class="sig-arg">eutils</span>=<span class="sig-default">None</span>)</span>
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<pre class="literalblock">
create a RecordSet interface for the set of database identifiers
Parameters are:
dbids -- a DBIds
dbtype -- the dbtype to use (EUtils.Config.{SEQUENCE,PUBLIATION}_TYPE)
in case dbids.db isn't in the list of know NCBI databases.
Defaults to None.
eutils -- the ThinClient to use, defaults to creating a new
ThinClient.ThinClient()
</pre>
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