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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
Module _index
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module _index</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html">source code</a></span></p>
<p>Dictionary like indexing of sequence files (PRIVATE).</p>
<p>You are not expected to access this module, or any of its code,
directly. This is all handled internally by the Bio.SeqIO.index(...)
function which is the public interface for this functionality.</p>
<p>The basic idea is that we scan over a sequence file, looking for new
record markers. We then try and extract the string that
Bio.SeqIO.parse/read would use as the record id, ideally without actually
parsing the full record. We then use a subclassed Python dictionary to
record the file offset for the record start against the record id.</p>
<p>Note that this means full parsing is on demand, so any invalid or
problem record may not trigger an exception until it is accessed. This is
by design.</p>
<p>This means our dictionary like objects have in memory ALL the keys
(all the record identifiers), which shouldn't be a problem even with
second generation sequencing. If this is an issue later on, storing the
keys and offsets in a temp lookup file might be one idea (e.g. using
SQLite or an OBDA style index).</p>
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html" class="summary-name" onclick="show_private();">_IndexedSeqFileDict</a><br />
Read only dictionary interface to a sequential sequence file.
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html" class="summary-name" onclick="show_private();">_SQLiteManySeqFilesDict</a><br />
Read only dictionary interface to many sequential sequence files.
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index.SeqFileRandomAccess-class.html" class="summary-name">SeqFileRandomAccess</a>
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index.SffRandomAccess-class.html" class="summary-name">SffRandomAccess</a><br />
Random access to a Standard Flowgram Format (SFF) file.
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index.SffTrimedRandomAccess-class.html" class="summary-name">SffTrimedRandomAccess</a>
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<a href="Bio.SeqIO._index.SequentialSeqFileRandomAccess-class.html" class="summary-name">SequentialSeqFileRandomAccess</a>
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<a href="Bio.SeqIO._index.GenBankRandomAccess-class.html" class="summary-name">GenBankRandomAccess</a><br />
Indexed dictionary like access to a GenBank file.
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<a href="Bio.SeqIO._index.EmblRandomAccess-class.html" class="summary-name">EmblRandomAccess</a><br />
Indexed dictionary like access to an EMBL file.
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<a href="Bio.SeqIO._index.SwissRandomAccess-class.html" class="summary-name">SwissRandomAccess</a><br />
Random access to a SwissProt file.
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<a href="Bio.SeqIO._index.UniprotRandomAccess-class.html" class="summary-name">UniprotRandomAccess</a><br />
Random access to a UniProt XML file.
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index.IntelliGeneticsRandomAccess-class.html" class="summary-name">IntelliGeneticsRandomAccess</a><br />
Random access to a IntelliGenetics file.
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO._index.TabRandomAccess-class.html" class="summary-name">TabRandomAccess</a><br />
Random access to a simple tabbed file.
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<a href="Bio.SeqIO._index.FastqRandomAccess-class.html" class="summary-name">FastqRandomAccess</a><br />
Random access to a FASTQ file (any supported variant).
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<a href="Bio.SeqIO._index-module.html#_FormatToRandomAccess" class="summary-name" onclick="show_private();">_FormatToRandomAccess</a> = <code title="{'ace': <class 'Bio.SeqIO._index.SequentialSeqFileRandomAccess'>,
'embl': <class 'Bio.SeqIO._index.EmblRandomAccess'>,
'fasta': <class 'Bio.SeqIO._index.SequentialSeqFileRandomAccess'>,
'fastq': <class 'Bio.SeqIO._index.FastqRandomAccess'>,
'fastq-illumina': <class 'Bio.SeqIO._index.FastqRandomAccess'>,
'fastq-sanger': <class 'Bio.SeqIO._index.FastqRandomAccess'>,
'fastq-solexa': <class 'Bio.SeqIO._index.FastqRandomAccess'>,
'gb': <class 'Bio.SeqIO._index.GenBankRandomAccess'>,
..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">ace</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.Seque<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.SeqIO'"><code class="variable-quote">'</code><code class="variable-string">Bio.SeqIO</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc">_FormatToRandomAccess</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">ace</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.SequentialSeqFileRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">embl</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.EmblRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">fasta</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.SequentialSeqFileRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">fastq</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.FastqRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">fastq-illumina</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.FastqRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">fastq-sanger</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.FastqRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">fastq-solexa</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.FastqRandomAccess'><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">gb</code><code class="variable-quote">'</code><code class="variable-op">: </code><class 'Bio.SeqIO._index.GenBankRandomAccess'><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
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