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<a href="Bio-module.html">Package Bio</a> ::
Package GenBank
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package GenBank</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Code to work with GenBank formatted files.
Classes:
Iterator Iterate through a file of GenBank entries
Dictionary Access a GenBank file using a dictionary interface.
ErrorFeatureParser Catch errors caused during parsing.
FeatureParser Parse GenBank data in Seq and SeqFeature objects.
RecordParser Parse GenBank data into a Record object.
NCBIDictionary Access GenBank using a dictionary interface.
_BaseGenBankConsumer A base class for GenBank consumer that implements
some helpful functions that are in common between
consumers.
_FeatureConsumer Create SeqFeature objects from info generated by
the Scanner
_RecordConsumer Create a GenBank record object from Scanner info.
_PrintingConsumer A debugging consumer.
ParserFailureError Exception indicating a failure in the parser (ie.
scanner or consumer)
LocationParserError Exception indiciating a problem with the spark based
location parser.
Functions:
search_for Do a query against GenBank.
download_many Download many GenBank records.
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<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser-module.html">Bio.GenBank.LocationParser</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record-module.html">Bio.GenBank.Record</a></strong>: <em class="summary">Hold GenBank data in a straightforward format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Scanner-module.html">Bio.GenBank.Scanner</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.utils-module.html">Bio.GenBank.utils</a></strong>: <em class="summary">Useful utilities for helping in parsing GenBank files.</em> </li>
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<span class="summary-type"> </span>
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<a href="Bio.GenBank.Iterator-class.html" class="summary-name">Iterator</a><br />
Iterator interface to move over a file of GenBank entries one at a
time.
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<span class="summary-type"> </span>
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<a href="Bio.GenBank.ParserFailureError-class.html" class="summary-name">ParserFailureError</a><br />
Failure caused by some kind of problem in the parser.
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<a href="Bio.GenBank.LocationParserError-class.html" class="summary-name">LocationParserError</a><br />
Could not Properly parse out a location from a GenBank file.
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<span class="summary-type"> </span>
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<a href="Bio.GenBank.FeatureParser-class.html" class="summary-name">FeatureParser</a><br />
Parse GenBank files into Seq + Feature objects.
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<span class="summary-type"> </span>
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<a href="Bio.GenBank.RecordParser-class.html" class="summary-name">RecordParser</a><br />
Parse GenBank files into Record objects
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<span class="summary-type"> </span>
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<a href="Bio.GenBank._BaseGenBankConsumer-class.html" class="summary-name" onclick="show_private();">_BaseGenBankConsumer</a><br />
Abstract GenBank consumer providing useful general functions.
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<span class="summary-type"> </span>
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<a href="Bio.GenBank._FeatureConsumer-class.html" class="summary-name" onclick="show_private();">_FeatureConsumer</a><br />
Create a SeqRecord object with Features to return.
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<a href="Bio.GenBank._RecordConsumer-class.html" class="summary-name" onclick="show_private();">_RecordConsumer</a><br />
Create a GenBank Record object from scanner generated information.
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<span class="summary-type"> </span>
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<a href="Bio.GenBank.NCBIDictionary-class.html" class="summary-name">NCBIDictionary</a><br />
Access GenBank using a read-only dictionary interface.
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<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a href="Bio.GenBank-module.html#search_for" class="summary-sig-name">search_for</a>(<span class="summary-sig-arg">search</span>,
<span class="summary-sig-arg">database</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">nucleotide</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">reldate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">mindate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">maxdate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">start_id</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">max_ids</span>=<span class="summary-sig-default">50000000</span>)</span><br />
search_for(search[, reldate][, mindate][, maxdate] [, batchsize][,
delay][, callback_fn][, start_id][, max_ids]) -> ids</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#search_for">source code</a></span>
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<span class="summary-type">handle of results</span>
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<td><span class="summary-sig"><a href="Bio.GenBank-module.html#download_many" class="summary-sig-name">download_many</a>(<span class="summary-sig-arg">ids</span>,
<span class="summary-sig-arg">database</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">nucleotide</code><code class="variable-quote">'</code></span>)</span><br />
Download many records from GenBank.</td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#download_many">source code</a></span>
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<span class="summary-type"> </span>
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<a name="GENBANK_INDENT"></a><span class="summary-name">GENBANK_INDENT</span> = <code title="12">12</code>
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<span class="summary-type"> </span>
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<a name="GENBANK_SPACER"></a><span class="summary-name">GENBANK_SPACER</span> = <code title="' '"><code class="variable-quote">'</code><code class="variable-string"> </code><code class="variable-quote">'</code></code>
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<a name="FEATURE_KEY_INDENT"></a><span class="summary-name">FEATURE_KEY_INDENT</span> = <code title="5">5</code>
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<a name="FEATURE_QUALIFIER_INDENT"></a><span class="summary-name">FEATURE_QUALIFIER_INDENT</span> = <code title="21">21</code>
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<span class="summary-type"> </span>
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<a name="FEATURE_KEY_SPACER"></a><span class="summary-name">FEATURE_KEY_SPACER</span> = <code title="' '"><code class="variable-quote">'</code><code class="variable-string"> </code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<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>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">search_for</span>(<span class="sig-arg">search</span>,
<span class="sig-arg">database</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">nucleotide</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">reldate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">mindate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">maxdate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">start_id</span>=<span class="sig-default">0</span>,
<span class="sig-arg">max_ids</span>=<span class="sig-default">50000000</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.GenBank-pysrc.html#search_for">source code</a></span>
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<p>search_for(search[, reldate][, mindate][, maxdate] [, batchsize][,
delay][, callback_fn][, start_id][, max_ids]) -> ids</p>
<p>Search GenBank and return a list of the GenBank identifiers (gi's)
that match the criteria. search is the search string used to search the
database. Valid values for database are 'nucleotide', 'protein',
'popset' and 'genome'. reldate is the number of dates prior to the
current date to restrict the search. mindate and maxdate are the dates
to restrict the search, e.g. 2002/01/01. start_id is the number to begin
retrieval on. max_ids specifies the maximum number of id's to
retrieve.</p>
<p>batchsize, delay and callback_fn are old parameters for compatibility
-- do not set them.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">download_many</span>(<span class="sig-arg">ids</span>,
<span class="sig-arg">database</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">nucleotide</code><code class="variable-quote">'</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#download_many">source code</a></span>
</td>
</tr></table>
<p>Download many records from GenBank. ids is a list of gis or
accessions.</p>
<p>callback_fn, broken_fn, delay, faildelay, batchsize, parser are old
parameter for compatibility. They should not be used.</p>
<dl class="fields">
<dt>Returns: handle of results</dt>
</dl>
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